Microbial Genomics
4.2K views | +0 today
Follow
Microbial Genomics
Microbial Genomics, Genomic Epidemiology, High-throughput Sequencing
Curated by Mark Pallen
Your new post is loading...
Your new post is loading...
Scooped by Mark Pallen
Scoop.it!

Cellulose mediates attachment of Salmonella enterica Serovar Typhimurium to tomatoes - Shaw - 2011 - Environmental Microbiology Reports - Wiley Online Library

Cellulose mediates attachment of Salmonella enterica Serovar Typhimurium to tomatoes - Shaw - 2011 - Environmental Microbiology Reports - Wiley Online Library | Microbial Genomics | Scoop.it

Fresh fruit and vegetables are important components of a healthy and balanced diet. However, they are increasingly being recognized as important vehicles for transmission of human pathogens that were traditionally classified as zoonotic. There is a significant gap in our knowledge and understanding of the mechanisms by which human pathogens colonize and survive on or in fruits and vegetables. In this study we investigated the binding of Salmonella enterica to tomato fruits (Solanum lycopersicum), which is becoming a major source of human infection. We report that Salmonella enterica serovars Typhimurium and Senftenberg bound to the surface of unripe tomatoes in an aggregative pattern, while serovar Thompson adhered diffusely. We found that while flagella did not have a role in binding, bcsC S. Typhimurim mutants, deficient in cellulose production, exhibited significantly reduced level of attachment to tomatoes. Trans complementation of the mutation restored adhesion to the wild-type level.

more...
No comment yet.
Scooped by Mark Pallen
Scoop.it!

Colonic mucosa-associated microbiota is influenced by an interaction of Crohn disease and FUT2 (Secretor) genotype

The FUT2 (Secretor) gene is responsible for the presence of ABO histo-blood group antigens on the gastrointestinal mucosa and in bodily secretions. Individuals lacking a functional copy of FUT2 are known as “nonsecretors” and display an array of differences in susceptibility to infection and disease, including Crohn disease. To determine whether variation in resident microbial communities with respect to FUT2 genotype is a potential factor contributing to susceptibility, we performed 454-based community profiling of the intestinal microbiota in a panel of healthy subjects and Crohn disease patients and determined their genotype for the primary nonsecretor allele in Caucasian populations, W143X (G428A). Consistent with previous studies, we observe significant deviations in the microbial communities of individuals with Crohn disease. Furthermore, the FUT2 genotype explains substantial differences in community composition, diversity, and structure, and we identified several bacterial species displaying disease-by-genotype associations. These findings indicate that alterations in resident microbial communities may in part explain the variety of host susceptibilities surrounding nonsecretor status and that FUT2 is an important genetic factor influencing host–microbial diversity.

more...
No comment yet.
Scooped by Mark Pallen
Scoop.it!

Sortase enzymes in Gram-positive bacteria - Spirig - Molecular Microbiology - Wiley Online Library

Sortase enzymes in Gram-positive bacteria - Spirig - Molecular Microbiology - Wiley Online Library | Microbial Genomics | Scoop.it

In Gram-positive bacteria proteins are displayed on the cell surface using sortase enzymes. These cysteine transpeptidases join proteins bearing an appropriate sorting signal to strategically positioned amino groups on the cell surface. Working alone, or in concert with other enzymes, sortases either attach proteins to the cross-bridge peptide of the cell wall or they link proteins together to form pili. Because surface proteins play a fundamental role in microbial physiology and are frequently virulence factors, sortase enzymes have been intensely studied since their discovery a little more than a decade ago. Based on their primary sequences and functions sortases can be partitioned into distinct families called class A to F enzymes. Most bacteria elaborate their surfaces using more than one type of sortase which function non-redundantly by recognizing unique sorting signals within their protein substrates. Here we review what is known about the functions of these enzymes and the molecular basis of catalysis. Particular emphasis is placed on ‘pilin’ specific class C sortases that construct structurally complex pili. Exciting new data has revealed that these enzymes are amazingly promiscuous in the substrates that they can employ and that there is a startling degree of diversity in their mechanism of action. We also review recent data that suggests that sortases are targeted to specific sites on the cell surface where they work with other sortases and accessory factors to properly function.

more...
No comment yet.
Scooped by Mark Pallen
Scoop.it!

LRB · Hugh Pennington · Smallpox Scares: Bioterrorism

LRB · Hugh Pennington · Smallpox Scares: Bioterrorism | Microbial Genomics | Scoop.it
After two or three days of illness, pains of extraordinary severity develop. The head feels as though the skull is opening and shutting. Excruciating backache feels like the bones grinding together.
more...
No comment yet.
Scooped by Mark Pallen
Scoop.it!

The Rough Guide to Evolution: The Rough Guide to Darwin

The Rough Guide to Evolution: The Rough Guide to Darwin | Microbial Genomics | Scoop.it

Talk given to doctoral students in Oxford 11th Oct 2011
Covers Darwin's early life, including wayward youth, before discussing his major work, impact and legacy

Warning: Explicit discussion of Darwin and sexuality. "Let's get Downe and dirty with Darwin!"

more...
No comment yet.
Scooped by Mark Pallen
Scoop.it!

PLoS ONE: Pyrosequencing-Based Analysis of the Mucosal Microbiota in Healthy Individuals Reveals Ubiquitous Bacterial Groups and Micro-Heterogeneity

PLoS ONE: Pyrosequencing-Based Analysis of the Mucosal Microbiota in Healthy Individuals Reveals Ubiquitous Bacterial Groups and Micro-Heterogeneity | Microbial Genomics | Scoop.it

his study used 16S rRNA-based pyrosequencing to examine the microbial community that is closely associated with the colonic mucosa of five healthy individuals. Spatial heterogeneity in microbiota was measured at right colon, left colon and rectum, and between biopsy duplicates spaced 1 cm apart. The data demonstrate that mucosal-associated microbiota is comprised of Firmicutes (50.9%±21.3%), Bacteroidetes (40.2%±23.8%) and Proteobacteria (8.6%±4.7%), and that interindividual differences were apparent. Among the genera, Bacteroides, Leuconostoc and Weissella were present at high abundance (4.6% to 41.2%) in more than 90% of the studied biopsy samples. Lactococcus, Streptococcus, Acidovorax, Acinetobacter, Blautia, Faecalibacterium, Veillonella, and several unclassified bacterial groups were also ubiquitously present at an abundance <7.0% of total microbial community. With the exception of one individual, the mucosal-associated microbiota was relatively homogeneous along the colon (average 61% Bray-Curtis similarity). However, micro-heterogeneity was observed in biopsy duplicates within defined colonic sites for three of the individuals. A weak but significant Mantel correlation of 0.13 was observed between the abundance of acidomucins and mucosal-associated microbiota (P-value = 0.04), indicating that the localized biochemical differences may contribute in part to the micro-heterogeneity. This study provided a detailed insight to the baseline mucosal microbiota along the colon, and revealed the existence of micro-heterogeneity within defined colonic sites for certain individuals.

more...
No comment yet.
Scooped by Mark Pallen
Scoop.it!

Genome Biol Evol -- Collected Resources : Chance and Necessity in Evolution from a meeting in Ravello, Italy, October 2010

Genome Biol Evol -- Collected Resources : Chance and Necessity in Evolution from a meeting in Ravello, Italy, October 2010 | Microbial Genomics | Scoop.it

Chance and Necessity in Evolution

Great collection of papers from a meeting in Ravello, Italy, October 2010

more...
No comment yet.
Scooped by Mark Pallen
Scoop.it!

Where Did the Term ‘Core Microbiome’ Come From?

Where Did the Term ‘Core Microbiome’ Come From? | Microbial Genomics | Scoop.it

In an excellent post about the vaginal microbiome (the microbes that in the vagina), Dr. Rad asks: I wonder if the idea of a ‘core microbiome’ came from Lourens Baas Becking’s oft-quoted dictum...

more...
No comment yet.
Scooped by Mark Pallen
Scoop.it!

Great Read at Birmingham

Great Read at Birmingham | Microbial Genomics | Scoop.it
Here are a few links to posts (and via them to videos) from the Rough Guide to Evolution blog relevant to the Great Read at Birmingham initiative.
more...
No comment yet.
Scooped by Mark Pallen
Scoop.it!

Chromosome Organization by a Nucleoid-Associated Protein in Live Bacteria

Bacterial chromosomes are confined in submicrometer-sized nucleoids. Chromosome organization is facilitated by nucleoid-associated proteins (NAPs), but the mechanisms of action remain elusive. In this work, we used super-resolution fluorescence microscopy, in combination with a chromosome-conformation capture assay, to study the distributions of major NAPs in live Escherichia coli cells. Four NAPs—HU, Fis, IHF, and StpA—were largely scattered throughout the nucleoid. In contrast, H-NS, a global transcriptional silencer, formed two compact clusters per chromosome, driven by oligomerization of DNA-bound H-NS through interactions mediated by the amino-terminal domain of the protein. H-NS sequestered the regulated operons into these clusters and juxtaposed numerous DNA segments broadly distributed throughout the chromosome. Deleting H-NS led to substantial chromosome reorganization. These observations demonstrate that H-NS plays a key role in global chromosome organization in bacteria.

more...
No comment yet.
Scooped by Mark Pallen
Scoop.it!

The bacterial actin MreB rotates, and rotation depends on cell-wall assembly

Bacterial cells possess multiple cytoskeletal proteins involved in a wide range of cellular processes. These cytoskeletal proteins are dynamic, but the driving forces and cellular functions of these dynamics remain poorly understood. Eukaryotic cytoskeletal dynamics are often driven by motor proteins, but in bacteria no motors that drive cytoskeletal motion have been identified to date. Here, we quantitatively study the dynamics of the Escherichia coli actin homolog MreB, which is essential for the maintenance of rod-like cell shape in bacteria. We find that MreB rotates around the long axis of the cell in a persistent manner. Whereas previous studies have suggested that MreB dynamics are driven by its own polymerization, we show that MreB rotation does not depend on its own polymerization but rather requires the assembly of the peptidoglycan cell wall. The cell-wall synthesis machinery thus either constitutes a novel type of extracellular motor that exerts force on cytoplasmic MreB, or is indirectly required for an as-yet-unidentified motor. Biophysical simulations suggest that one function of MreB rotation is to ensure a uniform distribution of new peptidoglycan insertion sites, a necessary condition to maintain rod shape during growth. These findings both broaden the view of cytoskeletal motors and deepen our understanding of the physical basis of bacterial morphogenesis.

more...
No comment yet.
Scooped by Mark Pallen
Scoop.it!

Vorsprung durch Technik: Open-source genomics of the German E. coli outbreak

A talk given at the University of Birmingham Open Day 10 Sept 2011 Further information on the topics covered in this talk can be found here: http://www.nejm....
more...
No comment yet.
Scooped by Mark Pallen
Scoop.it!

Bacterial Genome Sequencing Offers Latest Tool Against Diseases

Bacterial Genome Sequencing Offers Latest Tool Against Diseases | Microbial Genomics | Scoop.it
Investigators can now take precautions against diseases starting to emerge, like flu or food-borne bugs and antibiotic-resistant strains of bacteria.
more...
No comment yet.
Scooped by Mark Pallen
Scoop.it!

Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes : Nature Genetics : Nature Publishing Group

Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes : Nature Genetics : Nature Publishing Group | Microbial Genomics | Scoop.it
Roy Kishony and colleagues sequenced the genomes of 112 Burkholderia dolosa isolates recovered from 14 individuals with cystic fibrosis as part of a retrospective study from a hospital epidemic monitored over the course of 16 years.
more...
No comment yet.
Scooped by Mark Pallen
Scoop.it!

Mark Pallen on Ion Torrent and open-source genomics

Mark Pallen talking about the Ion Torrent PGM and its use in the open-source genomics analyses of the German epidemic strain of E. coli O104:H4. 

more...
No comment yet.
Scooped by Mark Pallen
Scoop.it!

Evidence of cellulose metabolism by the giant panda gut microbiome

The giant panda genome codes for all necessary enzymes associated with a carnivorous digestive system but lacks genes for enzymes needed to digest cellulose, the principal component of their bamboo diet. It has been posited that this iconic species must therefore possess microbial symbionts capable of metabolizing cellulose, but these symbionts have remained undetected. Here we examined 5,522 prokaryotic ribosomal RNA gene sequences in wild and captive giant panda fecal samples. We found lower species richness of the panda microbiome than of mammalian microbiomes for herbivores and nonherbivorous carnivores. We detected 13 operational taxonomic units closely related to Clostridium groups I and XIVa, both of which contain taxa known to digest cellulose. Seven of these 13 operational taxonomic units were unique to pandas compared with other mammals. Metagenomic analysis using ∼37-Mbp contig sequences from gut microbes recovered putative genes coding two cellulose-digesting enzymes and one hemicellulose-digesting enzyme, cellulase, β-glucosidase, and xylan 1,4-β-xylosidase, in Clostridium group I. Comparing glycoside hydrolase profiles of pandas with those of herbivores and omnivores, we found a moderate abundance of oligosaccharide-degrading enzymes for pandas (36%), close to that for humans (37%), and the lowest abundance of cellulases and endohemicellulases (2%), which may reflect low digestibility of cellulose and hemicellulose in the panda's unique bamboo diet. The presence of putative cellulose-digesting microbes, in combination with adaptations related to feeding, physiology, and morphology, show that giant pandas have evolved a number of traits to overcome the anatomical and physiological challenge of digesting a diet high in fibrous matter.

more...
No comment yet.
Scooped by Mark Pallen
Scoop.it!

Kunstformen der Natur: Stunning SciArt from over a century ago!

Kunstformen der Natur: Stunning SciArt from over a century ago! | Microbial Genomics | Scoop.it

Stunning SciArt from over a century ago!

http://en.wikipedia.org/wiki/Kunstformen_der_Natur

http://commons.wikimedia.org/wiki/Kunstformen_der_Natur 

more...
No comment yet.
Scooped by Mark Pallen
Scoop.it!

Distant Mimivirus relative with a larger genome highlights the fundamental features of Megaviridae

Mimivirus, a DNA virus infecting acanthamoeba, was for a long time the largest known virus both in terms of particle size and gene content. Its genome encodes 979 proteins, including the first four aminoacyl tRNA synthetases (ArgRS, CysRS, MetRS, and TyrRS) ever found outside of cellular organisms. The discovery that Mimivirus encoded trademark cellular functions prompted a wealth of theoretical studies revisiting the concept of virus and associated large DNA viruses with the emergence of early eukaryotes. However, the evolutionary significance of these unique features remained impossible to assess in absence of a Mimivirus relative exhibiting a suitable evolutionary divergence. Here, we present Megavirus chilensis, a giant virus isolated off the coast of Chile, but capable of replicating in fresh water acanthamoeba. Its 1,259,197-bp genome is the largest viral genome fully sequenced so far. It encodes 1,120 putative proteins, of which 258 (23%) have no Mimivirus homologs. The 594 Megavirus/Mimivirus orthologs share an average of 50% of identical residues. Despite this divergence, Megavirus retained all of the genomic features characteristic of Mimivirus, including its cellular-like genes. Moreover, Megavirus exhibits three additional aminoacyl-tRNA synthetase genes (IleRS, TrpRS, and AsnRS) adding strong support to the previous suggestion that the Mimivirus/Megavirus lineage evolved from an ancestral cellular genome by reductive evolution. The main differences in gene content between Mimivirus and Megavirus genomes are due to (i) lineages specific gains or losses of genes, (ii) lineage specific gene family expansion or deletion, and (iii) the insertion/migration of mobile elements (intron, intein).

more...
No comment yet.
Scooped by Mark Pallen
Scoop.it!

Frontiers | Acquired Antibiotic Resistance Genes: An Overview | Frontiers in Antimicrobials, Resistance and Chemotherapy

Frontiers | Acquired Antibiotic Resistance Genes: An Overview | Frontiers in Antimicrobials, Resistance and Chemotherapy | Microbial Genomics | Scoop.it

In this review an overview is given on antibiotic resistance (AR) mechanisms with special attentions to the AR genes described so far preceded by a short introduction on the discovery and mode of action of the different classes of antibiotics. As this review is only dealing with acquired resistance, attention is also paid to mobile genetic elements such as plasmids, transposons, and integrons, which are associated with AR genes, and involved in the dispersal of antimicrobial determinants between different bacteria.

more...
No comment yet.
Scooped by Mark Pallen
Scoop.it!

Translation of a minigene in the 5' leader sequenc... [Biochem J. 2011] - PubMed - NCBI

The 5' end of the major RNA transcript of the LEE1 operon of enterohaemorrhagic Escherichia coli contains ~170 bases before the AUG translation start codon of the first recognised gene, ler. This unusually long leader sequence carries three potential alternative AUG start codons. Using a lac fusion expression vector, we confirmed that the ler gene AUG is functional for translation initiation, and we checked for translation initiation at the three alternative AUG codons. Whilst two of the alternative AUG codons appear incompetent for translation initiation, we detected strong initiation at the third AUG, which is followed by one AAA codon and a UAG stop codon. The location of this very short two-codon open reading frame with respect to the ler translation start appears critical. Hence mutations that destroy the UAG stop codon, or short deletions between the UAG stop codon and the ler translation initiation region, result in big effects on ler expression. In the context of the full length LEE1 operon leader sequence, translation of this very short two-codon open reading frame is necessary for optimal expression of the ler gene and for the subsequent interactions of enterohaemorrhagic Escherichia coli with host target cells.

more...
No comment yet.
Scooped by Mark Pallen
Scoop.it!

Don't doubt the value of blogging in academic publishing

Don't doubt the value of blogging in academic publishing | Microbial Genomics | Scoop.it

Responding to Leonard Cassuto's recent blog post about the value blogging in academic publishing, Sarah-Louise Quinnell explains why a presence on social media is taking her career to the next level 

more...
No comment yet.
Scooped by Mark Pallen
Scoop.it!

Vorsprung durch Technik: talk at Prokagenomics 2011 in Göttingen, Germany

Vorsprung durch Technik: talk at Prokagenomics 2011 in Göttingen, Germany | Microbial Genomics | Scoop.it
http://youtu.be/HyN2BZPItrg...
more...
No comment yet.
Scooped by Mark Pallen
Scoop.it!

Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death

Although investigations of medieval plague victims have identified Yersinia pestis as the putative etiologic agent of the pandemic, methodological limitations have prevented large-scale genomic investigations to evaluate changes in the pathogen's virulence over time. We screened over 100 skeletal remains from Black Death victims of the East Smithfield mass burial site (1348–1350, London, England). Recent methods of DNA enrichment coupled with high-throughput DNA sequencing subsequently permitted reconstruction of ten full human mitochondrial genomes (16 kb each) and the full pPCP1 (9.6 kb) virulence-associated plasmid at high coverage. Comparisons of molecular damage profiles between endogenous human and Y. pestis DNA confirmed its authenticity as an ancient pathogen, thus representing the longest contiguous genomic sequence for an ancient pathogen to date. Comparison of our reconstructed plasmid against modern Y. pestis shows identity with several isolates matching the Medievalis biovar; however, our chromosomal sequences indicate the victims were infected with a Y. pestis variant that has not been previously reported. Our data reveal that the Black Death in medieval Europe was caused by a variant of Y. pestis that may no longer exist, and genetic data carried on its pPCP1 plasmid were not responsible for the purported epidemiological differences between ancient and modern forms of Y. pestis infections.

more...
No comment yet.
Scooped by Mark Pallen
Scoop.it!

Outbreak genomics : Nature Biotechnology : Nature Publishing Group

Whole-genome sequencing and crowdsourced analyses proved a powerful adjunct to traditional typing in the recent Escherichia coli outbreak.
more...
No comment yet.
Scooped by Mark Pallen
Scoop.it!

Structural diversity of bacterial flagellar motors : The EMBO Journal

Structural diversity of bacterial flagellar motors : The EMBO Journal | Microbial Genomics | Scoop.it

The bacterial flagellum is one of nature's most amazing and well-studied nanomachines. Its cell-wall-anchored motor uses chemical energy to rotate a microns-long filament and propel the bacterium towards nutrients and away from toxins. While much is known about flagellar motors from certain model organisms, their diversity across the bacterial kingdom is less well characterized, allowing the occasional misrepresentation of the motor as an invariant, ideal machine. Here, we present an electron cryotomographical survey of flagellar motor architectures throughout the Bacteria. While a conserved structural core was observed in all 11 bacteria imaged, surprisingly novel and divergent structures as well as different symmetries were observed surrounding the core. Correlating the motor structures with the presence and absence of particular motor genes in each organism suggested the locations of five proteins involved in the export apparatus including FliI, whose position below the C-ring was confirmed by imaging a deletion strain. The combination of conserved and specially-adapted structures seen here sheds light on how this complex protein nanomachine has evolved to meet the needs of different species.

more...
No comment yet.