W. Kittichotirat - Academia.edu (original) (raw)

Papers by W. Kittichotirat

Journal of Dental Research, 2015

Genome announcements, 2014

Mycoplasma hyosynoviae is a Gram-negative bacterium that can cause debilitating arthritis in swin... more Mycoplasma hyosynoviae is a Gram-negative bacterium that can cause debilitating arthritis in swine. Currently, there are no M. hyosynoviae genome sequences in the GenBank database, which makes it impossible to understand its pathogenesis, nutrition, or colonization characteristics, or to devise an effective strategy for its control. Here, we report the genome sequences of seven strains of M. hyosynoviae. Within each genome, several virulence factors were identified that may prove important in the pathogenesis of M. hyosynoviae-mediated arthritis and serve as potential virulence markers that may be critical in vaccine development.

Genome announcements, 2014

Mannheimia haemolytica is a Gram-negative bacterium and the principal etiological agent associate... more Mannheimia haemolytica is a Gram-negative bacterium and the principal etiological agent associated mostly with bovine respiratory disease complex. However, we report here the sequence of a strain with the novel A1/A6-cross-reactive serotype, strain PKL10, isolated from white-tailed deer. PKL10 was isolated from the spleen of farmed white-tailed deer showing clinical signs of pneumonia. The genome structure of PKL10 is dramatically different from that of previously sequenced isolates, which was demonstrated by genome alignments. In addition, the coding sequences in PKL10 share approximately 86% sequence identity with the coding sequences in other fully sequenced M. haemolytica strains. This suggests that PKL10 is a novel Mannheimia species.

Genome Announcements, 2014

Haemophilus parasuis is a normal commensal of the upper respiratory tract of healthy pigs. Howeve... more Haemophilus parasuis is a normal commensal of the upper respiratory tract of healthy pigs. However, in conjunction with stress and/or viral infections, or in immunocompromised animals, H. parasuis can transform into a pathogen causing Glasser's disease, which is typically characterized by fibrinous polyserositis, polyarthritis, meningitis, and sometimes acute pneumonia and septicemia. H. parasuis serotype 5 is highly virulent and more frequently isolated from respiratory and systemic infection in pigs. Recently Newport Laboratories isolated highly virulent H. parasuis serotype 4 strains from the tissues of diseased pigs. This study was undertaken to identify the genes responsible for H. parasuis serotype 4 virulence. To achieve this objective we performed genome-wide association studies (GWAS) across two virulent and three avirulent H. parasuis serotype 4 strains.

MicrobiologyOpen, 2015

Infection with Mycoplasma hyosynoviae can result in debilitating arthritis in pigs, particularly ... more Infection with Mycoplasma hyosynoviae can result in debilitating arthritis in pigs, particularly those aged 10 weeks or older. Strategies for controlling this pathogen are becoming increasingly important due to the rise in the number of cases of arthritis that have been attributed to infection in recent years. In order to begin to develop interventions to prevent arthritis caused by M. hyosynoviae, more information regarding the specific proteins and potential virulence factors that its genome encodes was needed. However, the genome of this emerging swine pathogen had not been sequenced previously. In this report, we present a comparative analysis of the genomes of seven strains of M. hyosynoviae isolated from different locations in North America during the years 2010 to 2013. We identified several putative virulence factors that may contribute to the ability of this pathogen to adhere to host cells. Additionally, we discovered several prophage genes present within the genomes of three strains that show significant similarity to MAV1, a phage isolated from the related species, M. arthritidis. We also identified CRISPR-Cas and type III restriction and modification systems present in two strains that may contribute to their ability to defend against phage infection.

PLoS ONE, 2011

Background: Aggregatibacter actinomycetemcomitans is genetically heterogeneous and comprises dist... more Background: Aggregatibacter actinomycetemcomitans is genetically heterogeneous and comprises distinct clonal lineages that may have different virulence potentials. However, limited information of the strain-to-strain genomic variations is available.

The Open Dentistry Journal, 2012

This study tested the feasibility of a high throughput metagenomic approach to analyze the pre-an... more This study tested the feasibility of a high throughput metagenomic approach to analyze the pre-and posttreatment of subgingival plaque in two subjects with aggressive periodontitis. DNA was extracted from subgingival samples and subjected to PCR amplification of the c2-c4 regions of the 16S rDNA using primers with bar codes to identify individual samples. The PCR products were pooled and sequenced for the v4 region of the 16S rDNA using the 454 FLX standard platform. The results were analyzed for species/phylotypes in the Human Oral Microbiome Database (HOMD) and Ribosomal Database Project (RDP) database. The sequencing of the amplicons resulted in 24,673 reads and identified 208 species/phylotypes. Of those, 129 species/phylotypes were identified in both patients but their proportions varied. While >120 species/phylotypes were identified in all samples, 28-42 species/phylotypes cumulatively represent 90% of all subgingival bacteria in each sample. The remaining species/phylotypes each constituted ≤0.2% of the total subgingival bacteria. In conclusion, the subgingival microbiota are characterized by high species richness dominated by a few species/phylotypes. The microbiota changed after periodontal therapy. High throughput metagenomic analysis is applicable to assess the complexity and changes of the subgingival microbiota.

PLoS ONE, 2013

The genome of periodontal pathogen Aggregatibacter actinomycetemcomitans exhibits substantial var... more The genome of periodontal pathogen Aggregatibacter actinomycetemcomitans exhibits substantial variations in gene content among unrelated strains primarily due to the presence or absence of genomic islands. This study examined the genomic stability of A. actinomycetemcomitans during its persistent infection in the same host. Four pairs of A. actinomycetemcomitans strains, each pair isolated from an individual over time (0-10 years), were examined for their gains/ losses of genes by whole genome sequencing, comparative genomic hybridization by microarray and PCR analysis. Possible effects due to genomic changes were further assessed by comparative transcriptome analysis using microarrays. The results showed that each pair of strains was clonally identical based on phylogenetic analysis of 150 core genes. A novel 24.1-Kb plasmid found in strain S23A was apparently lost in the sibling strain I23C. A 353-bp inversion affecting two essential genes of the serotype-specific gene cluster was found in the serotype antigen-nonexpressing strain I23C, while the same gene cluster was intact in the serotype-expressing sibling strain S23A. A 2,293-bp deletion affecting a gene encoding oxaloacetate decarboxylase and its neighbor region was found in strain SCC2302 but not in the sibling strain AAS4a. However, no evidence of gains or losses of genomic islands was found in the paired strains. Transcriptome profiles showed little or no difference in the paired strains. In conclusion, the genome of A. actinomycetemcomitans appears to be relatively stable during short-term infection. Several types of genomic changes were observed in the paired strains of A. actinomycetemcomitans recovered from the same subjects, including a mutation in serotype-specific gene cluster that may allow the bacteria to evade host immune response.

Nucleic Acids Research, 2009

Protinfo PPC' (Prediction of Protein Complex) is a web server that predicts atomic level structur... more Protinfo PPC' (Prediction of Protein Complex) is a web server that predicts atomic level structures of interacting proteins from their amino-acid sequences. It uses the interolog method to search for experimental protein complex structures that are homologous to the input sequences submitted by a user. These structures are then used as starting templates to generate protein complex models, which are returned to the user in Protein Data Bank format via email. The server supports modeling of both homo and hetero multimers and generally produces full atomic level models (including insertion/deletion regions) of protein complexes as long as at least one putative homologous template for the query sequences is found. The modeling pipeline behind Protinfo PPC has been rigorously benchmarked and proven to produce highly accurate protein complex models. The fully automated all atom comparative modeling service for protein complexes provided by Protinfo PPC server offers wide capabilities ranging from prediction of protein complex interactions to identification of possible interaction sites, which will be useful for researchers studying these topics. The Protinfo PPC web server is available at

Molecular Oral Microbiology, 2013

This chapter provides an overview of DNA microarrays. Microarrays are a technology in which 1000'... more This chapter provides an overview of DNA microarrays. Microarrays are a technology in which 1000's of nucleic acids are bound to a surface and are used to measure the relative concentration of nucleic acid sequences in a mixture via hybridization and subsequent detection of the hybridization events. We first cover the history of microarrays and the antecedent technologies that led to their development. We then discuss the methods of manufacture of microarrays and the most common biological applications. The chapter ends with a brief discussion of the limitations of microarrays and discusses how microarrays are being rapidly replaced by DNA sequencing technologies.

Journal of Bacteriology, 2012

Gram-negative Aggregatibacter actinomycetemcomitans can be distinguished (based on the promoter s... more Gram-negative Aggregatibacter actinomycetemcomitans can be distinguished (based on the promoter structure of the leukotoxin operon) into JP2 and non-JP2 genotypes, with the former found to be more pathogenic than the latter. Here we report the first complete genome sequence of a serotype b non-JP2 strain of A. actinomycetemcomitans.

Journal of Bacteriology, 2011

As part of a larger project to sequence multiple clinical isolates of Propionibacterium acnes, we... more As part of a larger project to sequence multiple clinical isolates of Propionibacterium acnes, we have produced a draft genome sequence of a novel Propionibacterium species that is closely related to, yet distinct (by sequence) from P. acnes. We have tentatively named this new species Propionibacterium humerusii.

Journal of Bacteriology, 2013

Journal of Bacteriology, 2009

Aggregatibacter actinomycetemcomitans is implicated in localized aggressive periodontitis. We rep... more Aggregatibacter actinomycetemcomitans is implicated in localized aggressive periodontitis. We report the first genome sequence of an A. actinomycetemcomitans strain isolated from an Old World primate.

Journal of Bacteriology, 2010

This report describes the genome sequences of Mannheimia haemolytica serotype A2 isolated from pn... more This report describes the genome sequences of Mannheimia haemolytica serotype A2 isolated from pneumonic lungs of two different ruminant species, one from Ovis aries, designated ovine (O), and the other from Bos taurus, designated bovine (B).

Journal of Bacteriology, 2010

The major clonal lineages of the Gram-negative periodontal pathogen Aggregatibacter actinomycetem... more The major clonal lineages of the Gram-negative periodontal pathogen Aggregatibacter actinomycetemcomitans include serotype a, b, and c strains. Here, we report the draft genome sequence of a naturally competent serotype a strain, D7S-1, isolated from a patient with aggressive periodontitis.

BMC Genomics, 2010

Background: Bacterial phenotype may be profoundly affected by the physical arrangement of their g... more Background: Bacterial phenotype may be profoundly affected by the physical arrangement of their genes in the genome. The Gram-negative species Aggregatibacter actinomycetemcomitans is a major etiologic agent of human periodontitis. Individual clonal types of A. actinomycetemcomitans may exhibit variable virulence and different patterns of disease association. This study examined the genome arrangement of A. actinomycetemcomitans using the genome sequences of serotypes a-c strains. The genome alignment and rearrangement were analyzed by the MAUVE and the GRIMM algorithms. The distribution patterns of genes along the leading/lagging strands were investigated. The occurrence and the location of repeat sequences relative to the genome rearrangement breakpoints were also determined.

BMC Genomics, 2010

Background: Mannhemia haemolytica is a Gram-negative bacterium and the principal etiological agen... more Background: Mannhemia haemolytica is a Gram-negative bacterium and the principal etiological agent associated with bovine respiratory disease complex. They transform from a benign commensal to a deadly pathogen, during stress such as viral infection and transportation to feedlots and cause acute pleuropneumonia commonly known as shipping fever. The U.S beef industry alone loses more than one billion dollars annually due to shipping fever. Despite its enormous economic importance there are no specific and accurate genetic markers, which will aid in understanding the pathogenesis and epidemiology of M. haemolytica at molecular level and assist in devising an effective control strategy. Description: During our comparative genomic sequence analysis of three Mannheimia haemolytica isolates, we identified a number of genes that are unique to each strain. These genes are "high value targets" for future studies that attempt to correlate the variable gene pool with phenotype. We also identified a number of high confidence single nucleotide polymorphisms (hcSNPs) spread throughout the genome and focused on non-synonymous SNPs in known virulence genes. These SNPs will be used to design new hcSNP arrays to study variation across strains, and will potentially aid in understanding gene regulation and the mode of action of various virulence factors. Conclusions: During our analysis we identified previously unknown possible type III secretion effector proteins, clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated sequences (Cas). The presence of CRISPR regions is indicative of likely co-evolution with an associated phage. If proven functional, the presence of a type III secretion system in M. haemolytica will help us re-evaluate our approach to study hostpathogen interactions. We also identified various adhesins containing immuno-dominant domains, which may interfere with host-innate immunity and which could potentially serve as effective vaccine candidates.

ABSTRACT Objective: The periodontal pathogen Aggregatibacter actinomycetemcomitans (Aa) displays ... more ABSTRACT Objective: The periodontal pathogen Aggregatibacter actinomycetemcomitans (Aa) displays significant genomic variations among strains. The genome content of each strain can be grouped into flexible gene pool and core gene pool. The functional significance of these strain-specific genes in the flexible gene pool remains to be determined. This study examined the role of flexible gene pool in the regulation of the growths of a wildtype biofilm-forming Aa strain and its non-fimbriated isogenic planktonic mutant. Methods: 5,690 gene clusters identified from the genomes of 6 Aa strains (two serotype a and one of each of serotype c, e and f, and the sequenced serotype b strain HK1651) were used to design and fabricate an Agilent custom microarray. A serotype a strain D7S and its isogenic non-fimbriated mutant strain D7SS were grown in trypticase soy broth at 37 oC in atmosphere supplemented with 5% CO2 for 12-18 hours until they reached OD650=0.2 and 0.4. The protocols for sample preparation, treatment, hybridization, and scanning were as described by the manufacturer (Agilent Technologies). Results: There were 144 and 500 upregulated (10-fold or higher in expression levels) and 135 and 500 downregulated (one-tenth or less in expression levels) genes of strain D7S in comparison to strain D7SS at OD650=0.2 and 0.4, respectively. The list of upregulated genes (N=108) of D7S in both growth densities included significant numbers of genes encoding hypothetical proteins and proteins of unknown functions. 80 of the upregulated 108 genes belong to the flexible gene pool of strain D7S. Conclusion: Specific sets of genes were up- and down-regulated in the growth of the wildtype Aa and the isogenic non-aggregating planktonic mutant. Strain-specific genes may play a role in aggregation and/or biofilm formation of Aa. Acknowledgements. This work was funded by NIDCR grant R01 DE012212

Journal of Dental Research, 2015

Genome announcements, 2014

Mycoplasma hyosynoviae is a Gram-negative bacterium that can cause debilitating arthritis in swin... more Mycoplasma hyosynoviae is a Gram-negative bacterium that can cause debilitating arthritis in swine. Currently, there are no M. hyosynoviae genome sequences in the GenBank database, which makes it impossible to understand its pathogenesis, nutrition, or colonization characteristics, or to devise an effective strategy for its control. Here, we report the genome sequences of seven strains of M. hyosynoviae. Within each genome, several virulence factors were identified that may prove important in the pathogenesis of M. hyosynoviae-mediated arthritis and serve as potential virulence markers that may be critical in vaccine development.

Genome announcements, 2014

Mannheimia haemolytica is a Gram-negative bacterium and the principal etiological agent associate... more Mannheimia haemolytica is a Gram-negative bacterium and the principal etiological agent associated mostly with bovine respiratory disease complex. However, we report here the sequence of a strain with the novel A1/A6-cross-reactive serotype, strain PKL10, isolated from white-tailed deer. PKL10 was isolated from the spleen of farmed white-tailed deer showing clinical signs of pneumonia. The genome structure of PKL10 is dramatically different from that of previously sequenced isolates, which was demonstrated by genome alignments. In addition, the coding sequences in PKL10 share approximately 86% sequence identity with the coding sequences in other fully sequenced M. haemolytica strains. This suggests that PKL10 is a novel Mannheimia species.

Genome Announcements, 2014

Haemophilus parasuis is a normal commensal of the upper respiratory tract of healthy pigs. Howeve... more Haemophilus parasuis is a normal commensal of the upper respiratory tract of healthy pigs. However, in conjunction with stress and/or viral infections, or in immunocompromised animals, H. parasuis can transform into a pathogen causing Glasser's disease, which is typically characterized by fibrinous polyserositis, polyarthritis, meningitis, and sometimes acute pneumonia and septicemia. H. parasuis serotype 5 is highly virulent and more frequently isolated from respiratory and systemic infection in pigs. Recently Newport Laboratories isolated highly virulent H. parasuis serotype 4 strains from the tissues of diseased pigs. This study was undertaken to identify the genes responsible for H. parasuis serotype 4 virulence. To achieve this objective we performed genome-wide association studies (GWAS) across two virulent and three avirulent H. parasuis serotype 4 strains.

MicrobiologyOpen, 2015

Infection with Mycoplasma hyosynoviae can result in debilitating arthritis in pigs, particularly ... more Infection with Mycoplasma hyosynoviae can result in debilitating arthritis in pigs, particularly those aged 10 weeks or older. Strategies for controlling this pathogen are becoming increasingly important due to the rise in the number of cases of arthritis that have been attributed to infection in recent years. In order to begin to develop interventions to prevent arthritis caused by M. hyosynoviae, more information regarding the specific proteins and potential virulence factors that its genome encodes was needed. However, the genome of this emerging swine pathogen had not been sequenced previously. In this report, we present a comparative analysis of the genomes of seven strains of M. hyosynoviae isolated from different locations in North America during the years 2010 to 2013. We identified several putative virulence factors that may contribute to the ability of this pathogen to adhere to host cells. Additionally, we discovered several prophage genes present within the genomes of three strains that show significant similarity to MAV1, a phage isolated from the related species, M. arthritidis. We also identified CRISPR-Cas and type III restriction and modification systems present in two strains that may contribute to their ability to defend against phage infection.

PLoS ONE, 2011

Background: Aggregatibacter actinomycetemcomitans is genetically heterogeneous and comprises dist... more Background: Aggregatibacter actinomycetemcomitans is genetically heterogeneous and comprises distinct clonal lineages that may have different virulence potentials. However, limited information of the strain-to-strain genomic variations is available.

The Open Dentistry Journal, 2012

This study tested the feasibility of a high throughput metagenomic approach to analyze the pre-an... more This study tested the feasibility of a high throughput metagenomic approach to analyze the pre-and posttreatment of subgingival plaque in two subjects with aggressive periodontitis. DNA was extracted from subgingival samples and subjected to PCR amplification of the c2-c4 regions of the 16S rDNA using primers with bar codes to identify individual samples. The PCR products were pooled and sequenced for the v4 region of the 16S rDNA using the 454 FLX standard platform. The results were analyzed for species/phylotypes in the Human Oral Microbiome Database (HOMD) and Ribosomal Database Project (RDP) database. The sequencing of the amplicons resulted in 24,673 reads and identified 208 species/phylotypes. Of those, 129 species/phylotypes were identified in both patients but their proportions varied. While >120 species/phylotypes were identified in all samples, 28-42 species/phylotypes cumulatively represent 90% of all subgingival bacteria in each sample. The remaining species/phylotypes each constituted ≤0.2% of the total subgingival bacteria. In conclusion, the subgingival microbiota are characterized by high species richness dominated by a few species/phylotypes. The microbiota changed after periodontal therapy. High throughput metagenomic analysis is applicable to assess the complexity and changes of the subgingival microbiota.

PLoS ONE, 2013

The genome of periodontal pathogen Aggregatibacter actinomycetemcomitans exhibits substantial var... more The genome of periodontal pathogen Aggregatibacter actinomycetemcomitans exhibits substantial variations in gene content among unrelated strains primarily due to the presence or absence of genomic islands. This study examined the genomic stability of A. actinomycetemcomitans during its persistent infection in the same host. Four pairs of A. actinomycetemcomitans strains, each pair isolated from an individual over time (0-10 years), were examined for their gains/ losses of genes by whole genome sequencing, comparative genomic hybridization by microarray and PCR analysis. Possible effects due to genomic changes were further assessed by comparative transcriptome analysis using microarrays. The results showed that each pair of strains was clonally identical based on phylogenetic analysis of 150 core genes. A novel 24.1-Kb plasmid found in strain S23A was apparently lost in the sibling strain I23C. A 353-bp inversion affecting two essential genes of the serotype-specific gene cluster was found in the serotype antigen-nonexpressing strain I23C, while the same gene cluster was intact in the serotype-expressing sibling strain S23A. A 2,293-bp deletion affecting a gene encoding oxaloacetate decarboxylase and its neighbor region was found in strain SCC2302 but not in the sibling strain AAS4a. However, no evidence of gains or losses of genomic islands was found in the paired strains. Transcriptome profiles showed little or no difference in the paired strains. In conclusion, the genome of A. actinomycetemcomitans appears to be relatively stable during short-term infection. Several types of genomic changes were observed in the paired strains of A. actinomycetemcomitans recovered from the same subjects, including a mutation in serotype-specific gene cluster that may allow the bacteria to evade host immune response.

Nucleic Acids Research, 2009

Protinfo PPC' (Prediction of Protein Complex) is a web server that predicts atomic level structur... more Protinfo PPC' (Prediction of Protein Complex) is a web server that predicts atomic level structures of interacting proteins from their amino-acid sequences. It uses the interolog method to search for experimental protein complex structures that are homologous to the input sequences submitted by a user. These structures are then used as starting templates to generate protein complex models, which are returned to the user in Protein Data Bank format via email. The server supports modeling of both homo and hetero multimers and generally produces full atomic level models (including insertion/deletion regions) of protein complexes as long as at least one putative homologous template for the query sequences is found. The modeling pipeline behind Protinfo PPC has been rigorously benchmarked and proven to produce highly accurate protein complex models. The fully automated all atom comparative modeling service for protein complexes provided by Protinfo PPC server offers wide capabilities ranging from prediction of protein complex interactions to identification of possible interaction sites, which will be useful for researchers studying these topics. The Protinfo PPC web server is available at

Molecular Oral Microbiology, 2013

This chapter provides an overview of DNA microarrays. Microarrays are a technology in which 1000'... more This chapter provides an overview of DNA microarrays. Microarrays are a technology in which 1000's of nucleic acids are bound to a surface and are used to measure the relative concentration of nucleic acid sequences in a mixture via hybridization and subsequent detection of the hybridization events. We first cover the history of microarrays and the antecedent technologies that led to their development. We then discuss the methods of manufacture of microarrays and the most common biological applications. The chapter ends with a brief discussion of the limitations of microarrays and discusses how microarrays are being rapidly replaced by DNA sequencing technologies.

Journal of Bacteriology, 2012

Gram-negative Aggregatibacter actinomycetemcomitans can be distinguished (based on the promoter s... more Gram-negative Aggregatibacter actinomycetemcomitans can be distinguished (based on the promoter structure of the leukotoxin operon) into JP2 and non-JP2 genotypes, with the former found to be more pathogenic than the latter. Here we report the first complete genome sequence of a serotype b non-JP2 strain of A. actinomycetemcomitans.

Journal of Bacteriology, 2011

As part of a larger project to sequence multiple clinical isolates of Propionibacterium acnes, we... more As part of a larger project to sequence multiple clinical isolates of Propionibacterium acnes, we have produced a draft genome sequence of a novel Propionibacterium species that is closely related to, yet distinct (by sequence) from P. acnes. We have tentatively named this new species Propionibacterium humerusii.

Journal of Bacteriology, 2013

Journal of Bacteriology, 2009

Aggregatibacter actinomycetemcomitans is implicated in localized aggressive periodontitis. We rep... more Aggregatibacter actinomycetemcomitans is implicated in localized aggressive periodontitis. We report the first genome sequence of an A. actinomycetemcomitans strain isolated from an Old World primate.

Journal of Bacteriology, 2010

This report describes the genome sequences of Mannheimia haemolytica serotype A2 isolated from pn... more This report describes the genome sequences of Mannheimia haemolytica serotype A2 isolated from pneumonic lungs of two different ruminant species, one from Ovis aries, designated ovine (O), and the other from Bos taurus, designated bovine (B).

Journal of Bacteriology, 2010

The major clonal lineages of the Gram-negative periodontal pathogen Aggregatibacter actinomycetem... more The major clonal lineages of the Gram-negative periodontal pathogen Aggregatibacter actinomycetemcomitans include serotype a, b, and c strains. Here, we report the draft genome sequence of a naturally competent serotype a strain, D7S-1, isolated from a patient with aggressive periodontitis.

BMC Genomics, 2010

Background: Bacterial phenotype may be profoundly affected by the physical arrangement of their g... more Background: Bacterial phenotype may be profoundly affected by the physical arrangement of their genes in the genome. The Gram-negative species Aggregatibacter actinomycetemcomitans is a major etiologic agent of human periodontitis. Individual clonal types of A. actinomycetemcomitans may exhibit variable virulence and different patterns of disease association. This study examined the genome arrangement of A. actinomycetemcomitans using the genome sequences of serotypes a-c strains. The genome alignment and rearrangement were analyzed by the MAUVE and the GRIMM algorithms. The distribution patterns of genes along the leading/lagging strands were investigated. The occurrence and the location of repeat sequences relative to the genome rearrangement breakpoints were also determined.

BMC Genomics, 2010

Background: Mannhemia haemolytica is a Gram-negative bacterium and the principal etiological agen... more Background: Mannhemia haemolytica is a Gram-negative bacterium and the principal etiological agent associated with bovine respiratory disease complex. They transform from a benign commensal to a deadly pathogen, during stress such as viral infection and transportation to feedlots and cause acute pleuropneumonia commonly known as shipping fever. The U.S beef industry alone loses more than one billion dollars annually due to shipping fever. Despite its enormous economic importance there are no specific and accurate genetic markers, which will aid in understanding the pathogenesis and epidemiology of M. haemolytica at molecular level and assist in devising an effective control strategy. Description: During our comparative genomic sequence analysis of three Mannheimia haemolytica isolates, we identified a number of genes that are unique to each strain. These genes are "high value targets" for future studies that attempt to correlate the variable gene pool with phenotype. We also identified a number of high confidence single nucleotide polymorphisms (hcSNPs) spread throughout the genome and focused on non-synonymous SNPs in known virulence genes. These SNPs will be used to design new hcSNP arrays to study variation across strains, and will potentially aid in understanding gene regulation and the mode of action of various virulence factors. Conclusions: During our analysis we identified previously unknown possible type III secretion effector proteins, clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated sequences (Cas). The presence of CRISPR regions is indicative of likely co-evolution with an associated phage. If proven functional, the presence of a type III secretion system in M. haemolytica will help us re-evaluate our approach to study hostpathogen interactions. We also identified various adhesins containing immuno-dominant domains, which may interfere with host-innate immunity and which could potentially serve as effective vaccine candidates.

ABSTRACT Objective: The periodontal pathogen Aggregatibacter actinomycetemcomitans (Aa) displays ... more ABSTRACT Objective: The periodontal pathogen Aggregatibacter actinomycetemcomitans (Aa) displays significant genomic variations among strains. The genome content of each strain can be grouped into flexible gene pool and core gene pool. The functional significance of these strain-specific genes in the flexible gene pool remains to be determined. This study examined the role of flexible gene pool in the regulation of the growths of a wildtype biofilm-forming Aa strain and its non-fimbriated isogenic planktonic mutant. Methods: 5,690 gene clusters identified from the genomes of 6 Aa strains (two serotype a and one of each of serotype c, e and f, and the sequenced serotype b strain HK1651) were used to design and fabricate an Agilent custom microarray. A serotype a strain D7S and its isogenic non-fimbriated mutant strain D7SS were grown in trypticase soy broth at 37 oC in atmosphere supplemented with 5% CO2 for 12-18 hours until they reached OD650=0.2 and 0.4. The protocols for sample preparation, treatment, hybridization, and scanning were as described by the manufacturer (Agilent Technologies). Results: There were 144 and 500 upregulated (10-fold or higher in expression levels) and 135 and 500 downregulated (one-tenth or less in expression levels) genes of strain D7S in comparison to strain D7SS at OD650=0.2 and 0.4, respectively. The list of upregulated genes (N=108) of D7S in both growth densities included significant numbers of genes encoding hypothetical proteins and proteins of unknown functions. 80 of the upregulated 108 genes belong to the flexible gene pool of strain D7S. Conclusion: Specific sets of genes were up- and down-regulated in the growth of the wildtype Aa and the isogenic non-aggregating planktonic mutant. Strain-specific genes may play a role in aggregation and/or biofilm formation of Aa. Acknowledgements. This work was funded by NIDCR grant R01 DE012212