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Microorganisms
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Bioinformatics and Omic Data Analysis in Microbial Research
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Bioinformatics and Omic Data Analysis in Microbial Research

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Microbiomes".

Deadline for manuscript submissions: 15 May 2025 | Viewed by 8522

Special Issue Editor

Prof. Dr. Douglas D. Rhoads

E-Mail Website
Guest Editor
1. Director of Interdisciplinary Graduate Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR 72701, USA
2. Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
Interests: genomics; molecular genetics in eukaryotes and prokaryotes; bacterial diseases affecting poultry.

Special Issue Information

Dear Colleagues,

This Special Issue explores the current applications of omics to understand the interplay/function of microbes in ecology, agriculture, disease, homeostasis, and industry. We solicit papers covering new research or reviews related to software development, pipeline development, or application of bioinformatics to address important current topics concerning microorganisms. Papers may focus on any group of microorganisms including viruses, bacteria, fungi, protists, etc., using bioinformatics to decipher biologically relevant understandings through genomics, proteomics, metabolomics, transcriptomics, or any combination. Given the important biological roles of microorganisms, the application of omics in these organisms is critical to elicit a deeper understanding. Relevant areas of interest might include speciation and species complexes, and pan genome analyses including gene transfer, gene networks, microbiomes, symbiosis and pathogenesis.

Prof. Dr. Douglas D. Rhoads
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • bioinformatics
  • microorganisms
  • genomics
  • proteomics
  • metabolomics
  • software pipelines

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Published Papers (7 papers)

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Research

19 pages, 2645 KiB  
Article
Staphylococcus aureus Proteins Implicated in the Reduced Virulence of sarA and sarA/agr Mutants in Osteomyelitis
by Karen E. Beenken, Mara J. Campbell, Stephanie D. Byrum, Rick D. Edmondson, Samuel G. Mackintosh, Alan J. Tackett and Mark S. Smeltzer
Microorganisms 2025, 13(1), 181; https://doi.org/10.3390/microorganisms13010181 - 16 Jan 2025
Viewed by 442
Abstract
Using a murine osteomyelitis model, we recently demonstrated that Staphylococcus aureus sarA and sarA/agr mutants generated in the USA300 strain LAC are attenuated to a greater extent than an isogenic agr mutant and that this can be attributed to a significant extent to [...] Read more.
Using a murine osteomyelitis model, we recently demonstrated that Staphylococcus aureus sarA and sarA/agr mutants generated in the USA300 strain LAC are attenuated to a greater extent than an isogenic agr mutant and that this can be attributed to a significant extent to the increased production of extracellular proteases in both mutants. Based on this, we used a mass-based proteomics approach to compare the proteomes of LAC, its isogenic agr, sarA, and sarA/agr mutants, and isogenic derivatives of all four of these strains unable to produce the extracellular proteases aureolysin, SspA, SspB, ScpA, or SplA-F. This allowed us to identify proteins that were present in reduced amounts in sarA, and sarA/agr mutants owing to the increased production of extracellular proteases. A total of 1039 proteins were detected in conditioned media (CM) from overnight cultures of LAC, and protease-mediated degradation was shown to contribute to the reduced abundance of 224 of these (21.6%) in CM from the sarA and sarA/agr mutants. Among these were specific proteins previously implicated in the pathogenesis and therapeutic recalcitrance of S. aureus osteomyelitis. This demonstrates that the ability of sarA to limit protease production plays a key role in post-translational remodeling of the S. aureus proteome to a degree that can be correlated with reduced virulence in our osteomyelitis model, and that it does so irrespective of the functional status of agr. This also suggests that at least some of these 224 proteins may be viable targets for prophylactic or therapeutic intervention. Full article
(This article belongs to the Special Issue Bioinformatics and Omic Data Analysis in Microbial Research)
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13 pages, 2086 KiB  
Article
Salmonella enterica serovar Schwarzengrund: Distribution, Virulence, and Antimicrobial Resistance
by Monique A. Felix, Jing Han, Bijay K. Khajanchi, Yasser M. Sanad, Shaohua Zhao and Steven L. Foley
Microorganisms 2025, 13(1), 92; https://doi.org/10.3390/microorganisms13010092 - 6 Jan 2025
Viewed by 652
Abstract
The global incidence of Salmonella enterica serovar Schwarzengrund has risen in recent years. This serotype has been isolated from poultry, retail meat, and other food products, leading to multiple outbreaks. Alongside the increase in infections, there are growing concerns about the increasing levels [...] Read more.
The global incidence of Salmonella enterica serovar Schwarzengrund has risen in recent years. This serotype has been isolated from poultry, retail meat, and other food products, leading to multiple outbreaks. Alongside the increase in infections, there are growing concerns about the increasing levels of antimicrobial resistance (AMR) among S. Schwarzengrund strains. This study aims to better understand the genetic factors possibly contributing to the rising prevalence of S. Schwarzengrund by analyzing the sequences of 2058 isolates from both human patients (N = 313) and food- and animal-associated sources, including chicken (N = 1145), turkey (N = 300), pork (N = 132), and other sources (N = 168). Data were obtained from GenBank and analyzed for AMR genes using AMRFinder. Additionally, putative virulence genes and plasmid transfer genes were assessed using the Virulence and AMR Plasmid Transfer Factor Database. AMR genes were found in 1269 (61.7%) of the isolates, with a total of 2478 AMR genes among the isolates, the most common being aph(3″)-Ib (N = 969, 47.1%), tet(A) (N = 190, 9.2%), and sul2 (N = 150, 7.3%), which are responsible for resistance to aminoglycoside, tetracycline, and sulfonamide, respectively. Additionally, 1060 (51.5%) isolates carried multiple plasmid transfer genes associated with IncFIB-FIC(FII) plasmids. Other plasmid types found in at least 1% of the strains included IncI1 (N = 101, 4.9%), IncHI2 (N = 62, 3.0%), or IncHI1 (N = 24, 1.2%). The virulence gene profiles of human isolates showed diversity but largely overlapped with those from different food sources. Notably, the aerobactin iron acquisition genes, associated with Salmonella’s virulence and colonization, were highly prevalent among chicken isolates (N = 1019, 89.0%) but less frequent in isolates from other sources (N = 65, 7.2%). IncFIB-FIC(FII) plasmids, commonly harboring the aerobactin operon, were highly prevalent among chicken-related isolates and present in about 10% of human isolates. The diverse plasmid, AMR, and virulence gene profiles in human-associated isolates suggest that multiple factors may contribute to the increased virulence in S. Schwarzengrund. Full article
(This article belongs to the Special Issue Bioinformatics and Omic Data Analysis in Microbial Research)
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17 pages, 12916 KiB  
Article
Directional and Strain-Specific Interaction Between Lactobacillus plantarum and Staphylococcus aureus
by Sandeep Kondakala, Sunghyun Yoon, Soumana Daddy Gaoh, Ohgew Kweon, Seong-Jae Kim and Mark E. Hart
Microorganisms 2024, 12(12), 2432; https://doi.org/10.3390/microorganisms12122432 - 26 Nov 2024
Viewed by 660
Abstract
The interaction between Lactobacillus plantarum and Staphylococcus aureus strains FRI-1169 and MN8, two original isolated strains from menstrual toxic shock syndrome (mTSS) cases, is a key focus for developing non-antibiotic strategies to control S. aureus-related infections. While the antagonistic effects of Lactobacilli [...] Read more.
The interaction between Lactobacillus plantarum and Staphylococcus aureus strains FRI-1169 and MN8, two original isolated strains from menstrual toxic shock syndrome (mTSS) cases, is a key focus for developing non-antibiotic strategies to control S. aureus-related infections. While the antagonistic effects of Lactobacilli species on S. aureus through mechanisms like organic acid and bacteriocin production are known, the molecular dynamics of these interactions remain underexplored. This study employs a proteomic approach to analyze the interactions between L. plantarum WCFS1 and S. aureus strains, FRI-1169 and MN8, during co-culture. We profiled differentially expressed proteins (DEPs) found in the spent media and cytosols of both bacteria, revealing distinct directional and strain-specific responses. The findings demonstrate that L. plantarum exerts a more pronounced effect on S. aureus, with more DEPs and upregulated proteins, while S. aureus showed fewer DEPs and more downregulated proteins. These strain-specific interactions highlight the complex metabolic and regulatory adjustments between these bacterial species. This research provides valuable insights into the molecular mechanisms of Lactobacillus-S. aureus antagonism and underscores the potential of proteomic analysis as a powerful tool for studying bacterial dynamics in co-culture systems. Full article
(This article belongs to the Special Issue Bioinformatics and Omic Data Analysis in Microbial Research)
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16 pages, 1518 KiB  
Article
Phylogenomic Analyses of Three Distinct Lineages Uniting Staphylococcus cohnii and Staphylococcus urealyticus from Diverse Hosts
by L. Caroline House, Amer Hasan, Andi Asnayanti, Adnan A. K. Alrubaye, Jeff Pummill and Douglas Rhoads
Microorganisms 2024, 12(8), 1549; https://doi.org/10.3390/microorganisms12081549 - 29 Jul 2024
Cited by 2 | Viewed by 1294
Abstract
We sequenced and assembled genomes for 17 isolates of Staphylococcus cohnii isolated from osteomyelitis lesions in young broilers from two separate experiments where we induced lameness using a hybrid wire-litter flooring system. Whole genome comparisons using three different methods support a close relationship [...] Read more.
We sequenced and assembled genomes for 17 isolates of Staphylococcus cohnii isolated from osteomyelitis lesions in young broilers from two separate experiments where we induced lameness using a hybrid wire-litter flooring system. Whole genome comparisons using three different methods support a close relationship of genomes from both S. cohnii and Staphylococcus urealyticus. The data support three different lineages, which we designated as Lineage 1, Lineage 2, and Lineage 3, uniting these two species within an evolving complex. We present evidence for horizontal transfer between lineages of genomic regions from 50–440 kbp. The transfer of a 186 kbp region from Lineage 1 to Lineage 2 appears to have generated Lineage 3. Human-associated isolates appear to be limited to Lineages 2 and 3 but Lineage 2 appears to contain a higher number of human pathogenic isolates. The chicken isolates from our lameness trials included genomically diverse isolates from both Lineage 1 and 2, and isolates from both lineages were obtained from osteomyelitis lesions of individual birds. Our results expand the diversity of Staphylococci associated with osteomyelitis in poultry and suggest a high diversity in the microbiome of day-old chicks. Our data also support a reevaluation and unification of the taxonomic classifications of S. cohnii and S. urealyticus. Full article
(This article belongs to the Special Issue Bioinformatics and Omic Data Analysis in Microbial Research)
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9 pages, 836 KiB  
Communication
Isolation and Genomic Analysis of a Case of Staphylococcus argenteus ST2250 Related to Sepsis in Italy
by Giulia Gatti, Francesca Taddei, Anna Marzucco, Maria Sofia Montanari, Giorgio Dirani, Silvia Zannoli, Laura Grumiro, Martina Brandolini, Claudia Colosimo, Laura Dionisi, Ludovica Ingletto, Alessandra Mistral De Pascali, Alessandra Scagliarini, Vittorio Sambri and Monica Cricca
Microorganisms 2024, 12(7), 1485; https://doi.org/10.3390/microorganisms12071485 - 20 Jul 2024
Viewed by 1252
Abstract
Staphylococcus argenteus, identified in 2006, represents a challenging case of bacterial taxonomic identification because of its high similarity to Staphylococcus aureus. In this context, neither mass spectrometry (MS) nor 16S gene analysis cannot precisely reveal the difference between the two species. [...] Read more.
Staphylococcus argenteus, identified in 2006, represents a challenging case of bacterial taxonomic identification because of its high similarity to Staphylococcus aureus. In this context, neither mass spectrometry (MS) nor 16S gene analysis cannot precisely reveal the difference between the two species. In our study, the sensitivity to antibiotics of S. argenteus isolated from blood culture was tested, and the investigation of the bacterial genome was performed by Multi-Locus Sequence Typing (MLST) and Whole-Genome Next-Generation Sequencing (WG-NGS). The pathogen was identified as ST2250 and presented perfectly matched resistance genes, namely aph(3′)-III, mgrA, and sepA, whereas the virulence gene detected was scn. Two plasmids were found: the pSAS plasmid, belonging to the family of Inc18, and plasmid pN315, belonging to the Rep3 group. The epidemiological distribution and the spread of S. argenteus infection are scarcely documented, particularly when associated with sepsis. Therefore, a correct taxonomy identification, antibiogram, and resistance gene analysis may help in acquiring knowledge about this bacterium and implement its detection and treatment. Full article
(This article belongs to the Special Issue Bioinformatics and Omic Data Analysis in Microbial Research)
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14 pages, 1945 KiB  
Article
Whole-Genome Deep Sequencing of the Healthy Adult Nasal Microbiome
by Mark Cannon, Gustavo Ferrer, Mari Tesch and Matthew Schipma
Microorganisms 2024, 12(7), 1407; https://doi.org/10.3390/microorganisms12071407 - 12 Jul 2024
Viewed by 2476
Abstract
This study aimed to determine shifts in microbial populations regarding richness and diversity from the daily use of a popular over-the-counter nasal spray. In addition, the finding of nasal commensal bacterial species that overlap with the oral microbiome may prove to be potential [...] Read more.
This study aimed to determine shifts in microbial populations regarding richness and diversity from the daily use of a popular over-the-counter nasal spray. In addition, the finding of nasal commensal bacterial species that overlap with the oral microbiome may prove to be potential probiotics for the “gateway microbiomes”. Nasal swab samples were obtained before and after using the most popular over-the-counter (OTC) nasal spray in 10 participants aged 18–48. All participants were healthy volunteers with no significant medical histories. The participants were randomly assigned a number by randomizing software and consisted of five men and five women. The sampling consisted of placing a nasal swab atraumatically into the nasal cavity. The samples were preserved and sent to Northwestern University Sequencing Center for whole-genome deep sequencing. After 21 days of OTC nasal spray use twice daily, the participants returned for further nasal microbiome sampling. The microbial analysis included all bacteria, archaea, viruses, molds, and yeasts via deep sequencing for species analysis. The Northwestern University Sequencing Center utilized artificial intelligence analysis to determine shifts in species and strains following nasal spray use that resulted in changes in diversity and richness. Full article
(This article belongs to the Special Issue Bioinformatics and Omic Data Analysis in Microbial Research)
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18 pages, 1418 KiB  
Article
Exploring Pathogen Presence Prediction in Pastured Poultry Farms through Transformer-Based Models and Attention Mechanism Explainability
by Athish Ram Das, Nisha Pillai, Bindu Nanduri, Michael J. Rothrock, Jr. and Mahalingam Ramkumar
Microorganisms 2024, 12(7), 1274; https://doi.org/10.3390/microorganisms12071274 - 23 Jun 2024
Viewed by 945
Abstract
In this study, we explore how transformer models, which are known for their attention mechanisms, can improve pathogen prediction in pastured poultry farming. By combining farm management practices with microbiome data, our model outperforms traditional prediction methods in terms of the F1 score—an [...] Read more.
In this study, we explore how transformer models, which are known for their attention mechanisms, can improve pathogen prediction in pastured poultry farming. By combining farm management practices with microbiome data, our model outperforms traditional prediction methods in terms of the F1 score—an evaluation metric for model performance—thus fulfilling an essential need in predictive microbiology. Additionally, the emphasis is on making our model’s predictions explainable. We introduce a novel approach for identifying feature importance using the model’s attention matrix and the PageRank algorithm, offering insights that enhance our comprehension of established techniques such as DeepLIFT. Our results showcase the efficacy of transformer models in pathogen prediction for food safety and mark a noteworthy contribution to the progress of explainable AI within the biomedical sciences. This study sheds light on the impact of effective farm management practices and highlights the importance of technological advancements in ensuring food safety. Full article
(This article belongs to the Special Issue Bioinformatics and Omic Data Analysis in Microbial Research)
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