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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Microbial Genetics and Genomics".

Deadline for manuscript submissions: closed (20 February 2022) | Viewed by 40434

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Special Issue Editor

Dr. Ir. Peter van Baarlen

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Guest Editor

Host-Microbe Interactions (HMI) Group, Department of Animal Sciences, Wageningen University and Research, Wageningen NL-6708 WD, The Netherlands
Interests: host–microbe interactions; (meta)-omics; infectious diseases; microbial contributions to host physiology; evolution of microbial traits; one health

Special Issue Information

Dear Colleagues,

The domestication of animals and plant breeding has supported the agricultural intensification that has allowed for huge human population sizes and economic growth. Plant and animal production in a changing world with increasing human populations is facing diverse challenges, including infectious diseases of plant crops and domestic animals. Disease-associated microbes, including bacteria, fungi and viruses, have been posing a major threat to agricultural production worldwide, and the increased use of antibiotics for the control of microbial pathogens has resulted in the global rise of antibiotic resistance. At present, old and new infectious diseases of plants, animals and humans continue to emerge, emphasising the need for novel approaches to detect, identify and control these diseases.

Genomics holds great promise for enhancing the detection and control of infectious diseases. For instance, farmers would welcome DNA-based on-farm tools for pathogen detection and taxonomic identification to determine the most appropriate control measures. Reduced antibiotic usage and the efficient control of infectious diseases require substantial knowledge of bacterial, viral and fungal genomes, including the presence of antibiotic resistance and virulence genes in microbial populations. Whole-genome sequencing of pathogenic microbes and metagenomics have been successfully used for the identification of the (horizontal) transmission and cycling of genes in microbial populations and have greatly aided the identification of virulence genes as well as infectious disease risk assessment and the prediction of antibiotic resistance. There is good scope to apply the metagenomic sequencing of DNA extracted from symptom-bearing plant parts, nasal swabs and fecal material to the detection of microbial disease-associated biomarker genes. This issue focuses on state-of-the-art omics work that is used to study pathogenic microbes of plants, animals and humans, as well as novel insights from this research and how these insights can be translated to practice.

Dr. Ir. Peter van Baarlen
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. Genes 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 2600 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

Infectious diseases of plants, animals and humans
Diagnostics
Outbreak predictions
Strain diversity
Spread of virulence genes in natural populations
Short-read sequencing
Long-read sequencing
In-field sequencing
Metagenomics
Resistome
Pathogenicity islands
Biosynthetic gene clusters
Virulence gene identification

Published Papers (11 papers)

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Editorial

Jump to: Research, Other

3 pages, 166 KiB

Open AccessEditorial

Special Issue “Omics Research of Pathogenic Microorganisms”

by Peter van Baarlen

Genes 2023, 14(6), 1229; https://doi.org/10.3390/genes14061229 - 07 Jun 2023

Viewed by 967

Abstract

Infectious diseases of plants, animals and humans pose a serious threat to global health and seriously impact ecosystem stability and agriculture, including food security [...] Full article

(This article belongs to the Special Issue Omics Research of Pathogenic Microorganisms)

Research

Jump to: Editorial, Other

19 pages, 540 KiB

Open AccessArticle

Using Functional Annotations to Study Pairwise Interactions in Urinary Tract Infection Communities

by Elena G. Lara, Isabelle van der Windt, Douwe Molenaar, Marjon G. J. de Vos and Chrats Melkonian

Genes 2021, 12(8), 1221; https://doi.org/10.3390/genes12081221 - 06 Aug 2021

Cited by 4 | Viewed by 3013

Abstract

The behaviour of microbial communities depends on environmental factors and on the interactions of the community members. This is also the case for urinary tract infection (UTI) microbial communities. Here, we devise a computational approach that uses indices of complementarity and competition based on metabolic gene annotation to rapidly predict putative interactions between pair of organisms with the aim to explain pairwise growth effects. We apply our method to 66 genomes selected from online databases, which belong to 6 genera representing members of UTI communities. This resulted in a selection of metabolic pathways with high correlation for each pairwise combination between a complementarity index and the experimentally derived growth data. Our results indicated that Enteroccus spp. were most complemented in its metabolism by the other members of the UTI community. This suggests that the growth of Enteroccus spp. can potentially be enhanced by complementary metabolites produced by other community members. We tested a few putative predicted interactions by experimental supplementation of the relevant predicted metabolites. As predicted by our method, folic acid supplementation led to the increase in the population density of UTI Enterococcus isolates. Overall, we believe our method is a rapid initial in silico screening for the prediction of metabolic interactions in microbial communities. Full article

(This article belongs to the Special Issue Omics Research of Pathogenic Microorganisms)

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15 pages, 3226 KiB

Open AccessEditor’s ChoiceArticle

Deciphering the Monilinia fructicola Genome to Discover Effector Genes Possibly Involved in Virulence

by Laura Vilanova, Claudio A. Valero-Jiménez and Jan A.L. van Kan

Genes 2021, 12(4), 568; https://doi.org/10.3390/genes12040568 - 14 Apr 2021

Cited by 22 | Viewed by 2586

Abstract

Brown rot is the most economically important fungal disease of stone fruits and is primarily caused by Monilinia laxa and Monlinia fructicola. Both species co-occur in European orchards although M. fructicola is considered to cause the most severe yield losses in stone fruit. This study aimed to generate a high-quality genome of M. fructicola and to exploit it to identify genes that may contribute to pathogen virulence. PacBio sequencing technology was used to assemble the genome of M. fructicola. Manual structural curation of gene models, supported by RNA-Seq, and functional annotation of the proteome yielded 10,086 trustworthy gene models. The genome was examined for the presence of genes that encode secreted proteins and more specifically effector proteins. A set of 134 putative effectors was defined. Several effector genes were cloned into Agrobacterium tumefaciens for transient expression in Nicotiana benthamiana plants, and some of them triggered necrotic lesions. Studying effectors and their biological properties will help to better understand the interaction between M. fructicola and its stone fruit host plants. Full article

(This article belongs to the Special Issue Omics Research of Pathogenic Microorganisms)

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18 pages, 3065 KiB

Open AccessArticle

Genome-Wide Identification of Genes Involved in Acid Stress Resistance of Salmonella Derby

by Dan Gu, Han Xue, Xiaohui Yuan, Jinyan Yu, Xiaomeng Xu, Yu Huang, Mingzhu Li, Xianyue Zhai, Zhiming Pan, Yunzeng Zhang and Xinan Jiao

Genes 2021, 12(4), 476; https://doi.org/10.3390/genes12040476 - 25 Mar 2021

Cited by 9 | Viewed by 2650

Abstract

Resistance to and survival under acidic conditions are critical for Salmonella to infect the host. As one of the most prevalent serotypes identified in pigs and humans, how S. Derby overcomes acid stress remains unclear. Here, we de novo sequenced the genome of a representative S. Derby strain 14T from our S. Derby strain stock and identified its acid resistance-associated genes using Tn-seq analysis. A total of 35 genes, including those belonging to two-component systems (TCS) (cpxAR), the CRISPR-Cas system (casCE), and other systems, were identified as essential for 14T to survive under acid stress. The results demonstrated that the growth curve and survival ability of ΔcpxA and ΔcpxR were decreased under acid stress, and the adhesion and invasion abilities to the mouse colon cancer epithelial cells (MC38) of ΔcpxR were also decreased compared with the wild type strain, suggesting that the TCS CpxAR plays an essential role in the acid resistance and virulence of S. Derby. Also, CasC and CasE were found to be responsible for acid resistance in S. Derby. Our results indicate that acid stress induces multiple genes’ expression to mediate the acid resistance of S. Derby and enhance its pathogenesis during an infection. Full article

(This article belongs to the Special Issue Omics Research of Pathogenic Microorganisms)

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10 pages, 1069 KiB

Open AccessArticle

Clonal Interference and Mutation Bias in Small Bacterial Populations in Droplets

by Philip Ruelens and J. Arjan G. M. de Visser

Genes 2021, 12(2), 223; https://doi.org/10.3390/genes12020223 - 04 Feb 2021

Cited by 3 | Viewed by 2730

Abstract

Experimental evolution studies have provided key insights into the fundamental mechanisms of evolution. One striking observation is that parallel and convergent evolution during laboratory evolution can be surprisingly common. However, these experiments are typically performed with well-mixed cultures and large effective population sizes, while pathogenic microbes typically experience strong bottlenecks during infection or drug treatment. Yet, our knowledge about adaptation in very small populations, where selection strength and mutation supplies are limited, is scant. In this study, wild-type and mutator strains of the bacterium Escherichia coli were evolved for about 100 generations towards increased resistance to the β-lactam antibiotic cefotaxime in millifluidic droplets of 0.5 µL and effective population size of approximately 27,000 cells. The small effective population size limited the adaptive potential of wild-type populations, where adaptation was limited to inactivating mutations, which caused the increased production of outer-membrane vesicles, leading to modest fitness increases. In contrast, mutator clones with an average of ~30-fold higher mutation rate adapted much faster by acquiring both inactivating mutations of an outer-membrane porin and particularly inactivating and gain-of-function mutations, causing the upregulation or activation of a common efflux pump, respectively. Our results demonstrate how in very small populations, clonal interference and mutation bias together affect the choice of adaptive trajectories by mediating the balance between high-rate and large-benefit mutations. Full article

(This article belongs to the Special Issue Omics Research of Pathogenic Microorganisms)

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24 pages, 2018 KiB

Open AccessArticle

CRISPR-Cas Diversity in Clinical Salmonella enterica Serovar Typhi Isolates from South Asian Countries

by Arif Mohammad Tanmoy, Chinmoy Saha, Mohammad Saiful Islam Sajib, Senjuti Saha, Florence Komurian-Pradel, Alex van Belkum, Rogier Louwen, Samir Kumar Saha and Hubert P. Endtz

Genes 2020, 11(11), 1365; https://doi.org/10.3390/genes11111365 - 18 Nov 2020

Cited by 9 | Viewed by 5614

Abstract

Typhoid fever, caused by Salmonella enterica serovar Typhi (S. Typhi), is a global health concern and its treatment is problematic due to the rise in antimicrobial resistance (AMR). Rapid detection of patients infected with AMR positive S. Typhi is, therefore, crucial to prevent further spreading. Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated genes (CRISPR-Cas), is an adaptive immune system that initially was used for typing purposes. Later, it was discovered to play a role in defense against phages and plasmids, including ones that carry AMR genes, and, at present, it is being explored for its usage in diagnostics. Despite the availability of whole-genome sequences (WGS), very few studied the CRISPR-Cas system of S. Typhi, let alone in typing purposes or relation to AMR. In the present study, we analyzed the CRISPR-Cas system of S. Typhi using WGS data of 1059 isolates obtained from Bangladesh, India, Nepal, and Pakistan in combination with demographic data and AMR status. Our results reveal that the S. Typhi CRISPR loci can be classified into two groups: A (evidence level >2) and B (evidence level ≤2), in which we identified a total of 47 unique spacers and 15 unique direct repeats. Further analysis of the identified spacers and repeats demonstrated specific patterns that harbored significant associations with genotype, demographic characteristics, and AMR status, thus raising the possibility of their usage as biomarkers. Potential spacer targets were identified and, interestingly, the phage-targeting spacers belonged to the group-A and plasmid-targeting spacers to the group-B CRISPR loci. Further analyses of the spacer targets led to the identification of an S. Typhi protospacer adjacent motif (PAM) sequence, TTTCA/T. New cas-genes known as DinG, DEDDh, and WYL were also discovered in the S. Typhi genome. However, a specific variant of the WYL gene was only identified in the extensively drug-resistant (XDR) lineage from Pakistan and ciprofloxacin-resistant lineage from Bangladesh. From this work, we conclude that there are strong correlations between variations identified in the S. Typhi CRISPR-Cas system and endemic AMR positive S. Typhi isolates. Full article

(This article belongs to the Special Issue Omics Research of Pathogenic Microorganisms)

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12 pages, 1081 KiB

Open AccessArticle

Transcriptome Analysis of Amyloodinium ocellatum Tomonts Revealed Basic Information on the Major Potential Virulence Factors

by Omkar Byadgi, Fabio Marroni, Ron Dirks, Michela Massimo, Donatella Volpatti, Marco Galeotti and Paola Beraldo

Genes 2020, 11(11), 1252; https://doi.org/10.3390/genes11111252 - 24 Oct 2020

Cited by 6 | Viewed by 2455

Abstract

The ectoparasite protozoan Amyloodinium ocellatum (AO) is the etiological agent of amyloodiniosis in European seabass (Dicentrarchus labrax) (ESB). There is a lack of information about basic molecular data on AO biology and its interaction with the host. Therefore, de novo transcriptome sequencing of AO tomonts was performed. AO trophonts were detached from infested ESB gills, and quickly becoming early tomonts were purified by Percoll^® density gradient. Tomont total RNA was processed and quality was assessed immediately. cDNA libraries were constructed using TruSeq^® Stranded mRNA kit and sequenced using Illumina sequencer. CLC assembly was used to generate the Transcriptome assembly of AO tomonts. Out of 48,188 contigs, 56.12% belong to dinophyceae wherein Symbiodinium microadriaticum had 94.61% similarity among dinophyceae. Functional annotations of contigs indicated that 12,677 had associated GO term, 9005 with KEGG term. The contigs belonging to dinophyceae resulted in the detection of several peptidases. A BLAST search for known virulent factors from the virulence database resulted in hits to Rab proteins, AP120, Ribosomal phosphoprotein, Heat-shock protein70, Casein kinases, Plasmepsin IV, and Brucipain. Hsp70 and casein kinase II alpha were characterized in-silico. Altogether, these results provide a reference database in understanding AO molecular biology, aiding to the development of novel diagnostics and future vaccines. Full article

(This article belongs to the Special Issue Omics Research of Pathogenic Microorganisms)

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15 pages, 2723 KiB

Open AccessFeature PaperArticle

Campylobacter jejuni Cas9 Modulates the Transcriptome in Caco-2 Intestinal Epithelial Cells

by Chinmoy Saha, Deborah Horst-Kreft, Inez Kross, Peter J. van der Spek, Rogier Louwen and Peter van Baarlen

Genes 2020, 11(10), 1193; https://doi.org/10.3390/genes11101193 - 14 Oct 2020

Cited by 11 | Viewed by 4947

Abstract

The zoonotic human pathogen Campylobacter jejuni is known for its ability to induce DNA-damage and cell death pathology in humans. The molecular mechanism behind this phenomenon involves nuclear translocation by Cas9, a nuclease in C. jejuni (CjeCas9) that is the molecular marker of the Type II CRISPR-Cas system. However, it is unknown via which cellular pathways CjeCas9 drives human intestinal epithelial cells into cell death. Here, we show that CjeCas9 released by C. jejuni during the infection of Caco-2 human intestinal epithelial cells directly modulates Caco-2 transcriptomes during the first four hours of infection. Specifically, our results reveal that CjeCas9 activates DNA damage (p53, ATM (Ataxia Telangiectasia Mutated Protein)), pro-inflammatory (NF-κB (Nuclear factor-κB)) signaling and cell death pathways, driving Caco-2 cells infected by wild-type C. jejuni, but not when infected by a cas9 deletion mutant, towards programmed cell death. This work corroborates our previous finding that CjeCas9 is cytotoxic and highlights on a RNA level the basal cellular pathways that are modulated. Full article

(This article belongs to the Special Issue Omics Research of Pathogenic Microorganisms)

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17 pages, 1867 KiB

Open AccessArticle

Comparison of Illumina versus Nanopore 16S rRNA Gene Sequencing of the Human Nasal Microbiota

by Astrid P. Heikema, Deborah Horst-Kreft, Stefan A. Boers, Rick Jansen, Saskia D. Hiltemann, Willem de Koning, Robert Kraaij, Maria A. J. de Ridder, Chantal B. van Houten, Louis J. Bont, Andrew P. Stubbs and John P. Hays

Genes 2020, 11(9), 1105; https://doi.org/10.3390/genes11091105 - 21 Sep 2020

Cited by 47 | Viewed by 11002

Abstract

Illumina and nanopore sequencing technologies are powerful tools that can be used to determine the bacterial composition of complex microbial communities. In this study, we compared nasal microbiota results at genus level using both Illumina and nanopore 16S rRNA gene sequencing. We also monitored the progression of nanopore sequencing in the accurate identification of species, using pure, single species cultures, and evaluated the performance of the nanopore EPI2ME 16S data analysis pipeline. Fifty-nine nasal swabs were sequenced using Illumina MiSeq and Oxford Nanopore 16S rRNA gene sequencing technologies. In addition, five pure cultures of relevant bacterial species were sequenced with the nanopore sequencing technology. The Illumina MiSeq sequence data were processed using bioinformatics modules present in the Mothur software package. Albacore and Guppy base calling, a workflow in nanopore EPI2ME (Oxford Nanopore Technologies—ONT, Oxford, UK) and an in-house developed bioinformatics script were used to analyze the nanopore data. At genus level, similar bacterial diversity profiles were found, and five main and established genera were identified by both platforms. However, probably due to mismatching of the nanopore sequence primers, the nanopore sequencing platform identified Corynebacterium in much lower abundance compared to Illumina sequencing. Further, when using default settings in the EPI2ME workflow, almost all sequence reads that seem to belong to the bacterial genus Dolosigranulum and a considerable part to the genus Haemophilus were only identified at family level. Nanopore sequencing of single species cultures demonstrated at least 88% accurate identification of the species at genus and species level for 4/5 strains tested, including improvements in accurate sequence read identification when the basecaller Guppy and Albacore, and when flowcell versions R9.4 (Oxford Nanopore Technologies—ONT, Oxford, UK) and R9.2 (Oxford Nanopore Technologies—ONT, Oxford, UK) were compared. In conclusion, the current study shows that the nanopore sequencing platform is comparable with the Illumina platform in detection bacterial genera of the nasal microbiota, but the nanopore platform does have problems in detecting bacteria within the genus Corynebacterium. Although advances are being made, thorough validation of the nanopore platform is still recommendable. Full article

(This article belongs to the Special Issue Omics Research of Pathogenic Microorganisms)

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