Genomic adaptation in the CAZyome and specialised metabolism of the plant-associated Streptomyces violaceusniger clade

Streptomycetes are Gram-positive actinobacteria largely represented in the plant root microbiota. The genetic determinants involved in the presence of Streptomyces in the rhizosphere are largely unknown and can rely on the ability to degrade plant-derived compounds such as cell-wall polysaccharides and on the production of specialised metabolites. To address whether Streptomyces strains recruited into root microbiota share genomic specificities related to these two functions, we engaged a comparative genomic analysis using a newly sequenced rhizospheric strain, Streptomyces sp. AgN23 and strains from the phylogenetically related S. violaceusniger clade. This analysis enlightens a shared prominent CAZyome potentially involved in plant polysaccharides degradation and a strong conservation of antimicrobials biosynthetic clusters (rustmicin, mediomycin, niphimycin, nigericin) as well as plant bioactive compounds (nigericin, echosides, elaiophylin). Taken together, our work supports the hypothesis that specific hydrolytic enzymes and specialised metabolites repertoires may play important roles in the development of Streptomyces strains in the rhizosphere.

Download Full-text

Comparative genomic analysis of Brevibacterium strains: insights into key genetic determinants involved in adaptation to the cheese habitat

BMC Genomics ◽

10.1186/s12864-017-4322-1 ◽

2017 ◽

Vol 18 (1) ◽

Cited By ~ 10

Author(s):

Nguyen-Phuong Pham ◽

Séverine Layec ◽

Eric Dugat-Bony ◽

Marie Vidal ◽

Françoise Irlinger ◽

...

Keyword(s):

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Comparative Genomic ◽

Genetic Determinants

Download Full-text

Comparative genomic analysis of Vibrios yields insights into genes associated with virulence towards C. gigas larvae

10.21203/rs.3.rs-18229/v2 ◽

2020 ◽

Author(s):

Hanna Kehlet-Delgado ◽

Claudia Häse ◽

Ryan S Mueller

Keyword(s):

Virulence Genes ◽

Genomic Analysis ◽

Comparative Genomic ◽

Genetic Determinants ◽

Orthologous Genes ◽

Protein Coding ◽

Disease Mechanisms ◽

General Survival ◽

Type 3 Secretion System ◽

Type 3

Abstract Background: Vibriosis has been implicated in major losses of larvae at shellfish hatcheries. However, the species of Vibrio responsible for disease in aquaculture settings and their associated virulence genes are often variable or undefined. Knowledge of the specific nature of these factors is essential to developing a better understanding of the environmental and biological conditions that lead to larvae mortality events in hatcheries. We tested the virulence of 51 Vibrio strains towards Pacific Oyster (Crassostreae gigas) larvae and sequenced draft genomes of 42 hatchery-associated vibrios to determine groups of orthologous genes associated with virulence and to determine the phylogenetic relationships among pathogens and non-pathogens of C. gigas larvae.Results: V. coralliilyticus strains were the most prevalent pathogenic isolates. A phylogenetic logistic regression model identified over 500 protein-coding genes correlated with pathogenicity. Many of these genes had straightforward links to disease mechanisms, including predicted hemolysins, proteases, and multiple Type 3 Secretion System genes, while others appear to have possible indirect roles in pathogenesis and may be more important for general survival in the host environment. Multiple metabolism and nutrient acquisition genes were also identified to correlate with pathogenicity, highlighting specific features that may enable pathogen survival within C. gigas larvae. Conclusions: These findings have important implications on the range of pathogenic Vibrio spp. found in oyster-rearing environments and the genetic determinants of virulence in these populations.

Download Full-text

Genome Mining of the Genus Streptacidiphilus for Biosynthetic and Biodegradation Potential

Genes ◽

10.3390/genes11101166 ◽

2020 ◽

Vol 11 (10) ◽

pp. 1166

Author(s):

Adeel Malik ◽

Yu Ri Kim ◽

Seung Bum Kim

Keyword(s):

Genome Mining ◽

Hydrolytic Enzymes ◽

Genomic Analysis ◽

Gene Clusters ◽

Enzymatic Activities ◽

Comparative Genomic ◽

New Members ◽

Genome Data ◽

The Family ◽

Promising Source

The genus Streptacidiphilus represents a group of acidophilic actinobacteria within the family Streptomycetaceae, and currently encompasses 15 validly named species, which include five recent additions within the last two years. Considering the potential of the related genera within the family, namely Streptomyces and Kitasatospora, these relatively new members of the family can also be a promising source for novel secondary metabolites. At present, 15 genome data for 11 species from this genus are available, which can provide valuable information on their biology including the potential for metabolite production as well as enzymatic activities in comparison to the neighboring taxa. In this study, the genome sequences of 11 Streptacidiphilus species were subjected to the comparative analysis together with selected Streptomyces and Kitasatospora genomes. This study represents the first comprehensive comparative genomic analysis of the genus Streptacidiphilus. The results indicate that the genomes of Streptacidiphilus contained various secondary metabolite (SM) producing biosynthetic gene clusters (BGCs), some of them exclusively identified in Streptacidiphilus only. Several of these clusters may potentially code for SMs that may have a broad range of bioactivities, such as antibacterial, antifungal, antimalarial and antitumor activities. The biodegradation capabilities of Streptacidiphilus were also explored by investigating the hydrolytic enzymes for complex carbohydrates. Although all genomes were enriched with carbohydrate-active enzymes (CAZymes), their numbers in the genomes of some strains such as Streptacidiphilus carbonis NBRC 100919T were higher as compared to well-known carbohydrate degrading organisms. These distinctive features of each Streptacidiphilus species make them interesting candidates for future studies with respect to their potential for SM production and enzymatic activities.

Download Full-text

Comparative genomic analysis of Vibrios yields insights into genes associated with virulence towards C. gigas larvae

10.21203/rs.3.rs-18229/v1 ◽

2020 ◽

Author(s):

Hanna Kehlet-Delgado ◽

Claudia Häse ◽

Ryan S Mueller

Keyword(s):

Virulence Genes ◽

Genomic Analysis ◽

Comparative Genomic ◽

Genetic Determinants ◽

Orthologous Genes ◽

Protein Coding ◽

Disease Mechanisms ◽

General Survival ◽

Type 3 Secretion System ◽

Type 3

Abstract Background: Vibriosis has been implicated in major losses of larvae at shellfish hatcheries. However, the species of Vibrio responsible for disease in aquaculture settings and their associated virulence genes are often variable or undefined. Knowledge of the specific nature of these factors is essential to developing a better understanding of the environmental and biological conditions that lead to larvae mortality events in hatcheries. We tested the virulence of 51 Vibrio strains towards Pacific Oyster (Crassostreae gigas) larvae and sequenced draft genomes of 42 hatchery-associated vibrios to determine groups of orthologous genes associated with virulence and to determine the phylogenetic relationships among pathogens and non-pathogens of C. gigas larvae.Results: V. coralliilyticus strains were the most prevalent pathogenic isolates. A phylogenetic logistic regression model identified over 500 protein-coding genes correlated with pathogenicity. Many of these genes had straightforward links to disease mechanisms, including predicted hemolysins, proteases, and multiple Type 3 Secretion System genes, while others appear to have possible indirect roles in pathogenesis and may be more important for general survival in the host environment. Multiple metabolism and nutrient acquisition genes were also identified to correlate with pathogenicity, highlighting specific features that may enable pathogen survival within C. gigas larvae. Conclusions: These findings have important implications on the range of pathogenic Vibrio sp. found in oyster-rearing environments and the genetic determinants of virulence in these populations.

Download Full-text

Comparative genomic analysis of Staphylococcus aureus CC80 strains. (c2015)

10.26756/th.2015.34 ◽

2015 ◽

Author(s):

Melhem E. Bilen

Keyword(s):

Staphylococcus Aureus ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Comparative Genomic

Download Full-text

Faculty Opinions recommendation of Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1108969.575120 ◽

2008 ◽

Author(s):

David Alpers

Keyword(s):

Pure Culture ◽

Bifidobacterium Longum ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Comparative Genomic ◽

Culture Growth

Download Full-text

Comparative Genomic Analysis of 450 Strains of Salmonella enterica Isolated from Diseased Animals

Genes ◽

10.3390/genes11091025 ◽

2020 ◽

Vol 11 (9) ◽

pp. 1025

Author(s):

Shaohua Zhao ◽

Cong Li ◽

Chih-Hao Hsu ◽

Gregory H. Tyson ◽

Errol Strain ◽

...

Keyword(s):

Resistance Genes ◽

Bacterial Infections ◽

Genomic Analysis ◽

Heavy Metal Resistance ◽

Metal Resistance ◽

Comparative Genomic ◽

Salmonella Infections ◽

Antimicrobial Resistance Genes ◽

Salmonella Pathogenicity Islands ◽

Shed Light

Salmonella is a leading cause of bacterial infections in animals and humans. We sequenced a collection of 450 Salmonella strains from diseased animals to better understand the genetic makeup of their virulence and resistance features. The presence of Salmonella pathogenicity islands (SPIs) varied by serotype. S. Enteritidis carried the most SPIs (n = 15), while S. Mbandaka, S. Cerro, S. Meleagridis, and S. Havana carried the least (n = 10). S. Typhimurium, S. Choleraesuis, S. I 4,5,12:i:-, and S. Enteritidis each contained the spv operon on IncFII or IncFII-IncFIB hybrid plasmids. Two S. IIIa carried a spv operon with spvD deletion on the chromosome. Twelve plasmid types including 24 hybrid plasmids were identified. IncA/C was frequently associated with S. Newport (83%) and S. Agona (100%) from bovine, whereas IncFII (100%), IncFIB (100%), and IncQ1 (94%) were seen in S. Choleraesuis from swine. IncX (100%) was detected in all S. Kentucky from chicken. A total of 60 antimicrobial resistance genes (ARGs), four disinfectant resistances genes (DRGs) and 33 heavy metal resistance genes (HMRGs) were identified. The Salmonella strains from sick animals contained various SPIs, resistance genes and plasmid types based on the serotype and source of the isolates. Such complicated genomic structures shed light on the strain characteristics contributing to the severity of disease and treatment failures in Salmonella infections, including those causing illnesses in animals.

Download Full-text

Pathogenic Determinants of the Mycobacterium kansasii Complex: An Unsuspected Role for Distributive Conjugal Transfer

Microorganisms ◽

10.3390/microorganisms9020348 ◽

2021 ◽

Vol 9 (2) ◽

pp. 348

Author(s):

Florian Tagini ◽

Trestan Pillonel ◽

Claire Bertelli ◽

Katia Jaton ◽

Gilbert Greub

Keyword(s):

Genomic Analysis ◽

Comparative Genomic ◽

Mycobacterium Kansasii ◽

Type Vii Secretion ◽

A Genome ◽

Genes Encoding ◽

Associated Proteins ◽

Immunosuppressed Patients ◽

Type Vii Secretion System ◽

Clinical Records

The Mycobacterium kansasii species comprises six subtypes that were recently classified into six closely related species; Mycobacterium kansasii (formerly M. kansasii subtype 1), Mycobacterium persicum (subtype 2), Mycobacterium pseudokansasii (subtype 3), Mycobacterium ostraviense (subtype 4), Mycobacterium innocens (subtype 5) and Mycobacterium attenuatum (subtype 6). Together with Mycobacterium gastri, they form the M. kansasii complex. M. kansasii is the most frequent and most pathogenic species of the complex. M. persicum is classically associated with diseases in immunosuppressed patients, and the other species are mostly colonizers, and are only very rarely reported in ill patients. Comparative genomics was used to assess the genetic determinants leading to the pathogenicity of members of the M. kansasii complex. The genomes of 51 isolates collected from patients with and without disease were sequenced and compared with 24 publicly available genomes. The pathogenicity of each isolate was determined based on the clinical records or public metadata. A comparative genomic analysis showed that all M. persicum, M. ostraviense, M innocens and M. gastri isolates lacked the ESX-1-associated EspACD locus that is thought to play a crucial role in the pathogenicity of M. tuberculosis and other non-tuberculous mycobacteria. Furthermore, M. kansasii was the only species exhibiting a 25-Kb-large genomic island encoding for 17 type-VII secretion system-associated proteins. Finally, a genome-wide association analysis revealed that two consecutive genes encoding a hemerythrin-like protein and a nitroreductase-like protein were significantly associated with pathogenicity. These two genes may be involved in the resistance to reactive oxygen and nitrogen species, a required mechanism for the intracellular survival of bacteria. Three non-pathogenic M. kansasii lacked these genes likely due to two distinct distributive conjugal transfers (DCTs) between M. attenuatum and M. kansasii, and one DCT between M. persicum and M. kansasii. To our knowledge, this is the first study linking DCT to reduced pathogenicity.

Download Full-text