scholarly journals Natural phage communities crosslink different species within the genus Staphylococcus

2021 ◽  
Author(s):  
Pauline Goeller ◽  
Tabea Elsener ◽  
Dominique Lorgé ◽  
Natasa Radulovic ◽  
Viona Bernardi ◽  
...  
Keyword(s):  
Drug Resistance ◽  
High Resolution ◽  
Host Range ◽  
Bacterial Communities ◽  
Phage Genome ◽  
Genetic Material ◽  
Interaction Matrix ◽  
Genome Diversity ◽  
Dominant Trait ◽  
Multiple Species

Abstract The importance of the bacteriophage host range builds on its role as an innate barrier, which defines the phages’ impact on bacterial communities and genome diversity. Yet, little is known about host range natural patterns. We characterize 94 novel staphylococcal phages from wastewater and establish their host range on a diversified panel of 117 staphylococci from 29 species. Using this high-resolution phage-bacteria interaction matrix, we unveil a multi-species host range as a dominant trait of the isolated staphylococcal phages. Phage genome sequencing shows this pattern to prevail irrespective of taxonomy. Network analysis between phage-infected bacteria revealed that hosts from multiple species, ecosystems, and drug-resistance phenotypes share numerous phages. This could promote genetic mobilization facilitated by many transfer routes. Lastly, we demonstrate that phages throughout this network package foreign genetic material at various frequencies. Our findings defy a strong host specialism of phages and highlight great possibilities for horizontal gene transfer.

scholarly journals Multi-species host range of staphylococcal phages isolated from wastewater

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Pauline C. Göller ◽  
Tabea Elsener ◽  
Dominic Lorgé ◽  
Natasa Radulovic ◽  
Viona Bernardi ◽  
...  
Keyword(s):  
Host Range ◽  
Bacterial Communities ◽  
Phage Genome ◽  
Genetic Material ◽  
Interaction Matrix ◽  
Genome Diversity ◽  
Dominant Trait ◽  
Resistance Marker ◽  
Antibiotic Resistance Marker ◽  
Multiple Species

AbstractThe host range of bacteriophages defines their impact on bacterial communities and genome diversity. Here, we characterize 94 novel staphylococcal phages from wastewater and establish their host range on a diversified panel of 117 staphylococci from 29 species. Using this high-resolution phage-bacteria interaction matrix, we unveil a multi-species host range as a dominant trait of the isolated staphylococcal phages. Phage genome sequencing shows this pattern to prevail irrespective of taxonomy. Network analysis between phage-infected bacteria reveals that hosts from multiple species, ecosystems, and drug-resistance phenotypes share numerous phages. Lastly, we show that phages throughout this network can package foreign genetic material enclosing an antibiotic resistance marker at various frequencies. Our findings indicate a weak host specialism of the tested phages, and therefore their potential to promote horizontal gene transfer in this environment.

scholarly journals DNA Extraction and Host Depletion Methods Significantly Impact and Potentially Bias Bacterial Detection in a Biological Fluid

mSystems ◽  
2021 ◽  
Author(s):  
Erika Ganda ◽  
Kristen L. Beck ◽  
Niina Haiminen ◽  
Justin D. Silverman ◽  
Ban Kawas ◽  
...  
Keyword(s):  
Food Safety ◽  
Dna Extraction ◽  
Bacterial Communities ◽  
Biological Fluid ◽  
Genetic Material ◽  
Next Generation ◽  
Microbial Composition ◽  
Chemical Methods ◽  
Bacterial Detection ◽  
Do So

Tracking the bacterial communities present in our food has the potential to inform food safety and product origin. To do so, the entire genetic material present in a sample is extracted using chemical methods or commercially available kits and sequenced using next-generation platforms to provide a snapshot of the microbial composition.

scholarly journals High-resolution sweep metagenomics using fast probabilistic inference

2018 ◽  
Author(s):  
Tommi Mäklin ◽  
Teemu Kallonen ◽  
Sophia David ◽  
Christine J. Boinett ◽  
Ben Pascoe ◽  
...  
Keyword(s):  
High Resolution ◽  
False Positive ◽  
Bacterial Communities ◽  
Probabilistic Inference ◽  
Detection Accuracy ◽  
Probabilistic Modelling ◽  
Sequencing Data ◽  
Close Relatives ◽  
Major Pathogens ◽  
Positive Results

AbstractDetermining the composition of bacterial communities beyond the level of a genus or species is challenging because of the considerable overlap between genomes representing close relatives. Here, we present the mSWEEP method for identifying and estimating the relative abundances of bacterial lineages from plate sweeps of enrichment cultures. mSWEEP leverages biologically grouped sequence assembly databases, applying probabilistic modelling, and provides controls for false positive results. Using sequencing data from major pathogens, we demonstrate significant improvements in lineage quantification and detection accuracy. Our method facilitates investigating cultures comprising mixtures of bacteria, and opens up a new field of plate sweep metagenomics.

scholarly journals Labour sharing promotes coexistence in atrazine degrading bacterial communities

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Loren Billet ◽  
Marion Devers ◽  
Nadine Rouard ◽  
Fabrice Martin-Laurent ◽  
Aymé Spor
Keyword(s):  
Bacterial Communities ◽  
Gene Loss ◽  
Bacterial Species ◽  
Single Species ◽  
Microbial Consortia ◽  
The Public ◽  
Herbicide Atrazine ◽  
Set Up ◽  
Multiple Species ◽  
Isolated Species

AbstractMicrobial communities are pivotal in the biodegradation of xenobiotics including pesticides. In the case of atrazine, multiple studies have shown that its degradation involved a consortia rather than a single species, but little is known about how interdependency between the species composing the consortium is set up. The Black Queen Hypothesis (BQH) formalized theoretically the conditions leading to the evolution of dependency between species: members of the community called ‘helpers’ provide publicly common goods obtained from the costly degradation of a compound, while others called ‘beneficiaries’ take advantage of the public goods, but lose access to the primary resource through adaptive degrading gene loss. Here, we test whether liquid media supplemented with the herbicide atrazine could support coexistence of bacterial species through BQH mechanisms. We observed the establishment of dependencies between species through atrazine degrading gene loss. Labour sharing between members of the consortium led to coexistence of multiple species on a single resource and improved atrazine degradation potential. Until now, pesticide degradation has not been approached from an evolutionary perspective under the BQH framework. We provide here an evolutionary explanation that might invite researchers to consider microbial consortia, rather than single isolated species, as an optimal strategy for isolation of xenobiotics degraders.

scholarly journals High-Throughput Analysis of Human Cytomegalovirus Genome Diversity Highlights the Widespread Occurrence of Gene-Disrupting Mutations and Pervasive Recombination

2015 ◽  
Vol 89 (15) ◽  
pp. 7673-7695 ◽  
Author(s):  
Steven Sijmons ◽  
Kim Thys ◽  
Mirabeau Mbong Ngwese ◽  
Ellen Van Damme ◽  
Jan Dvorak ◽  
...  
Keyword(s):  
High Resolution ◽  
Human Cytomegalovirus ◽  
Severe Disabilities ◽  
Host Immune System ◽  
Full Genome ◽  
Genome Diversity ◽  
Genome Sequences ◽  
Widespread Occurrence ◽  
Strain Diversity ◽  
Human Herpesviruses

ABSTRACTHuman cytomegalovirus is a widespread pathogen of major medical importance. It causes significant morbidity and mortality in immunocompromised individuals, and congenital infections can result in severe disabilities or stillbirth. Development of a vaccine is prioritized, but no candidate is close to release. Although correlations of viral genetic variability with pathogenicity are suspected, knowledge about the strain diversity of the 235-kb genome is still limited. In this study, 96 full-length human cytomegalovirus genomes from clinical isolates were characterized, quadrupling the amount of information available for full-genome analysis. These data provide the first high-resolution map of human cytomegalovirus interhost diversity and evolution. We show that cytomegalovirus is significantly more divergent than all other human herpesviruses and highlight hot spots of diversity in the genome. Importantly, 75% of strains are not genetically intact but contain disruptive mutations in a diverse set of 26 genes, including the immunomodulatory genes UL40 and UL111A. These mutants are independent of culture passage artifacts and circulate in natural populations. Pervasive recombination, which is linked to the widespread occurrence of multiple infections, was found throughout the genome. The recombination density was significantly higher than those of other human herpesviruses and correlated with strain diversity. While the overall effects of strong purifying selection on virus evolution are apparent, evidence of diversifying selection was found in several genes encoding proteins that interact with the host immune system, including UL18, UL40, UL142, and UL147. These residues may present phylogenetic signatures of past and ongoing virus-host interactions.IMPORTANCEHuman cytomegalovirus has the largest genome of all viruses that infect humans. Currently, there is a great interest in establishing associations between genetic variants and strain pathogenicity of this herpesvirus. Since the number of publicly available full-genome sequences is limited, knowledge about strain diversity is highly fragmented and biased toward a small set of loci. Combined with our previous work, we have now contributed 101 complete genome sequences. We have used these data to conduct the first high-resolution analysis of interhost genome diversity, providing an unbiased and comprehensive overview of cytomegalovirus variability. These data are of major value to the development of novel antivirals and a vaccine and to identify potential targets for genotype-phenotype experiments. Furthermore, these data have enabled a thorough study of the evolutionary processes that have shaped cytomegalovirus diversity.

scholarly journals Host Range Restriction of Epstein-Barr Virus and Related Lymphocryptoviruses

2015 ◽  
Vol 89 (17) ◽  
pp. 9133-9136 ◽  
Author(s):  
Janine Mühe ◽  
Fred Wang
Keyword(s):  
B Cells ◽  
Host Range ◽  
Epstein Barr Virus ◽  
Nonhuman Primates ◽  
Range Restriction ◽  
Barr Virus ◽  
Epstein Barr ◽  
Multiple Species ◽  
High Degree ◽  
Host Range Restriction

Epstein-Barr-related herpesviruses, or lymphocryptoviruses (LCV), naturally infect humans and nonhuman primates (NHP), but their host range is not well characterized. Using LCV and B cells from multiple species of Hominidae and Cercopithecidae, we show that LCV can immortalize B cells from some nonnative species but that growth transformation is restricted to B cells from their own family of hominoids or Old World NHP, suggesting a high degree of LCV adaptation to their natural primate host.

scholarly journals Late Quaternary climate change from δ18O records of multiple species of planktonic foraminifera: High-resolution records from the Anoxic Cariaco Basin, Venezuela

1997 ◽  
Vol 12 (3) ◽  
pp. 415-427 ◽  
Author(s):  
Hui-Ling Lin ◽  
Larry C. Peterson ◽  
Jonathan T. Overpeck ◽  
Susan E. Trumbore ◽  
David W. Murray
Keyword(s):  
Climate Change ◽  
High Resolution ◽  
Late Quaternary ◽  
Planktonic Foraminifera ◽  
Cariaco Basin ◽  
Quaternary Climate ◽  
Multiple Species

scholarly journals Rapid Detection of Common HIV-1 Drug Resistance Mutations by Use of High-Resolution Melting Analysis and Unlabeled Probes

2016 ◽  
Vol 55 (1) ◽  
pp. 122-133 ◽  
Author(s):  
David Sacks ◽  
Johanna Ledwaba ◽  
Lynn Morris ◽  
Gillian M. Hunt
Keyword(s):  
Drug Resistance ◽  
High Resolution ◽  
High Resolution Melting ◽  
Antiretroviral Drugs ◽  
High Resolution Melting Analysis ◽  
Resistance Mutations ◽  
Drug Resistance Mutations ◽  
Melting Analysis ◽  
Analytical Sensitivities ◽  
Hiv 1

ABSTRACTHIV rapidly accumulates resistance mutations following exposure to subtherapeutic concentrations of antiretroviral drugs that reduces treatment efficacy. High-resolution melting analysis (HRMA) has been used to successfully identify single nucleotide polymorphisms (SNPs) and to genotype viral and bacterial species. Here, we tested the ability of HRMA incorporating short unlabeled probes to accurately assign drug susceptibilities at the 103, 181, and 184 codons of the HIV-1 reverse transcriptase gene. The analytical sensitivities of the HRMA assays were 5% of mixed species for K103N and Y181C and 20% for M184V. When applied to 153 HIV-1 patient specimens previously genotyped by Sanger population sequencing, HRMA correctly assigned drug sensitivity or resistance profiles to 80% of the samples at codon 103 (K103K/N) (Cohen's kappa coefficient [κ] > 0.6;P< 0.05), 90% at 181 (Y181Y/C) (κ > 0.74,P< 0.05), and 80% at 184 (M184M/V) (κ > 0.62;P< 0.05). The frequency of incorrect genotypes was very low (≤1 to 2%) for each assay, which in most cases was due to the higher sensitivity of the HRMA assay. Specimens for which drug resistance profiles could not be assigned (9 to 20%) often had polymorphisms in probe binding regions. Thus, HRMA is a rapid, inexpensive, and sensitive method for the determination of drug sensitivities caused by major HIV-1 drug resistance mutations and, after further development to minimize the melting effects of nontargeted polymorphisms, may be suitable for surveillance purposes.

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