Amazing new fungus video

An interesting new video of fungal cells has been made.

The video shows millions of nuclei flowing through the tube-like filaments, or hyphae, of a single fungus cell (of the species Neurospora crassa). 

To see the video, click here.

The video was produced as part of a study by UCLA mathematician Marcus Roper's research group that was the first to measure and explain this dynamic movement of nuclei in the cells of a fungus.

More details about the fungus are provided in the following paper:

M. Roper, A. Simonin, P. C. Hickey, A. Leeder, N. L. Glass. Nuclear dynamics in a fungal chimera. Proceedings of the National Academy of Sciences, 2013; DOI: 10.1073/pnas.1220842110

Posted by Tim Sandle

Probiotics can help fight Salmonella infections

New research has revealed how a probiotic bacterium used to treat irritable bowel syndrome can soothe gut bacterial infections caused by Salmonella.

Probiotics are types of 'good' or 'benefical' bacteria. As well as aiding the immune system and digestion, scientists thunk that mixtures of pro biotic bacteria can help to reduce the growth of certain types of bacteria. Due to this, scientists are looking at the right types of probiotic bacteria.

Specifically, microbiologists have been studying a probiotic strain of Escherichia coli (not all strains of E. coli are harmful). A research group have found that a type of E. coli (called Nissle 1917 or Mutaflor) reduces Salmonella colonization by competing with the pathogen for iron, an essential nutrient that salmonella acquires in the gut in order to replicate at high levels.

Types of Salmonella bacteria can potentially cause illnesses such as typhoid fever, paratyphoid fever, and other food borne illness. Most persons infected with Salmonella develop diarrhea, fever, and abdominal cramps 12 to 72 hours after infection.

For many decades E. coli Nissle 1917 strain has been administered to patients with a variety of bowel disorders (such as ulcerative colitis and Crohn’s disease). It now appears that this beneficvial bacterium could be used to treat other types of disease.

The study was conducted by UC Irvine microbiologists and the findings have been published in the journal Cell Host & Microbe, in a paper titled "Probiotic Bacteria Reduce Salmonella Typhimurium Intestinal Colonization by Competing for Iron."

Posted by Tim Sandle

FDA issues fecal transplant guidance

The U.S. Food and Drug Administration (FDA) has issued a guidance note about fecal transplants. A fecal transplant involves transferring the stool of a healthy person into the gut of someone with an antibiotic resistant microbe infection.

Fecal transplants (or 'fecal bacteriotherapy') appear to have a high success rate. The technique aims to restore the balance between good bacteria and bad bacteria in the colon.

The success rate was studied recently in the New England Journal of Medicine, where the process was concluded to be successful in curing 15 out of 16 patients suffering from a recurrent diarrheal infection of the problem microbe Clostridium difficile. This bacterium is one of the so-called problem bacteria, noted for being resistant to many antibiotics.

To work, the technique requires fecal matter to be transferred to the patient being transplanted through a series of enemas. With the New England study, the transplants were compared with administrations of the he antibiotic vancomycin, and the transplants worked more effectively.

In light of the success rate, the Digital Journal reported that the the American Gastroenterological Association regards fecal transplants as "a promising treatment.".

Given that fecal transplants are being tried more often, the U.S. FDA has decided that the transplants require review and regulation. The FDA has declared that fecal transplants meet the definition of a biologic therapy. This means that researchers who want to perform the procedure will now have to submit an investigational new drug (IND) application, via the FDA. To aid medics, the FDA this week released a guidance note.

One stipulation that the FDA requires is that the treating physician obtains adequate informed consent from the patient or his or her legally authorized representative before therapy begins.

Posted by Tim Sandle

Microbiology of the skin: glossary of terms

Here is a useful glossary of terms relating to the microbiology of human skin:

• Keratinocyte
  The predominant cell type of the epidermis. 
  Keratinocytes produce keratin as they terminally differentiate into the squames of the stratum corneum
• Squame
  An enucleated, dead, squamous keratinocyte that is shed from the stratum corneum
• Sebum
  The oily, lipid-containing substance that is secreted by the sebaceous glands of the skin.
  Sebaceous glands are connected to the hair follicle and form the pilosebaceous unit. Sebum protects and emolliates the skin and hair
• 16S ribosomal RNA metagenomic sequencing. 
  Genomic analysis of 16S ribosomal RNA phylotypes from DNA that is extracted directly from bacterial communities in clinical or environmental samples, a process that circumvents culturing
• Microbiome
  All of the genetic material of a microbial community sequenced together
• Phylotype
  A taxon-neutral way to describe organisms based on their phylogenetic relationships to other organisms. 
  Phylotypes are determined by comparing 16S ribosomal RNA gene sequences. A common threshold used to define species-level phylotypes is 97% sequence identity of the 16S rRNA gene sequence
  Whole-genome shotgun metagenomic sequencing
  Genomic analysis of DNA that is extracted directly from a clinical or environmental sample and whole-genome shotgun (WGS) sequenced to represent the full microbiome
• Pattern recognition receptor (PRR)
  A receptor present on the surface of keratinocytes and other cells of the innate immune system that recognizes microorganism-specific molecules (for example, lipopolysaccharide and flagellin)
  
  

  

  
  
  
  
• Pathogen-associated molecular pattern (PAMP)
  A molecule that is associated with a pathogen and recognized by a pathogen recognition receptor. Examples include lipopolysaccharide, flagellin, lipoteichoic acid, double-stranded RNA, peptidoglycan and unmethylated CpG motifs
• Atopic dermatitis (AD)
  A type of eczema characterized by red, flaky, itchy skin, typically affecting the inner elbows and behind the knees. It is often associated with other atopic diseases such as allergic rhinitis, hay fever and asthma
• Seborrhoeic dermatitis
  An inflammatory, hyperproliferative skin condition characterized by red, flaky, skin often affecting sebaceous areas of the face, scalp and trunk. Commonly known as dandruff

Posted by Tim Sandle

Antimicrobial compounds from natural sources

There is an interesting paper by Hayashi et al, titled "Antimicrobial compounds from natural sources" and published by Frontiers. Here the authors present several scientific studies mainly focused on natural products with antimicrobial activity, which are the case of the natural antimicrobial peptides (AMPs) and host defense peptides (HDPs).

This discussion includes recent studies on the roles of honey hydrogen peroxide in antimicrobial activity against resistant microbial strains, as well as the use of essential oils for food preservation. The piece also includes a review of different  sources, including plants, terrestrial and sea animals; as well as other sources like coal or lignite, which may provide future antimicrobial compounds candidates.

The article can be viewed online here.

Posted by Tim Sandle

Microbial diversity

The tree of life is dominated by microbes, but many large branches remain uncharted because scientists have been historically restricted to studying the small fraction of species that will grow in a lab, according to the Scientist.

An international team of scientists has now begun to redress this bias, sequencing full genomes from single cells to bring the “uncultured majority” into view. In total, the team identified more than 200 new microbial species belonging to 29 underrepresented or unknown lineages. By sequencing DNA directly from environmental samples, geneticists have suggested that the two microbial domains of life—bacteria and archaea—include at least 60 major lineages (phyla), but just four of these account for more than 88 percent of cultivated microbes.

For further details, refer to the following paper:

C. Rinke et al., “Insights into the phylogeny and coding potential of microbial dark matter,” Nature, doi:10.1038/nature12352, 2013

Posted by Tim Sandle

Validating a microbial ID system for cleanroom bacteria

A new paper of interest has been published. The paper concerns the validation of a phenotypic microbial identification system to understand how efficiently the system works with cleanroom bacteria. Although the paper concerns a specific system (the GEN III OmniLog® ID System), the paper is designed to act as a case study.

The paper has been published in the European Journal of Parenteral & Pharmaceutical Sciences.

The abstract reads:

“Accurate microbial identification is of importance in assessing product and environmental risks in pharmaceutical manufacturing. Identification is important to assess the origin of contamination and to formulate corrective actions for contamination events. Many of the systems available either require manual manipulation and subjectivity in reading, and are, therefore, prone to errors, or consist of databases than err towards the clinical setting. This paper outlines the validation steps for the evaluation of a microbial identification system capable of screening industrial microflora: the GEN III OmniLog® ID System.”

The reference is:

Tim Sandle, Kerry Skinner, Jennifer Sandle, Barbara Gebala, Pavitra Kothandaraman (2013): Evaluation of the GEN III OmniLog® ID System microbial identification system for the profiling of cleanroom bacteria, European Journal of Parenteral & Pharmaceutical Sciences 18(2): 44-50

Posted by Tim Sandle

Pathoscope: new method to rapidly identify pathogens

Researchers from Boston University School of Medicine (BUSM) and George Washington University (GWU) have developed a method to rapidly identify pathogenic species and strains causing illnesses, such as pneumonia, that could help lead to earlier detection of disease outbreaks. The method has been termed the 'Pathoscope'.

This has been made possible through sequencing technologies that have advanced the collection of genomic data for bioforensics, biosurveillance and for use in clinical settings.

The pathoscope sequencing method is designed allow for rapid screening of thousands of infectious pathogens simultaneously, while being sensitive enough to monitor disease outbreaks caused by specific pathogenic strains.

The findings are featured online in the journal Genome Research. The reference is:

Owen E. Francis, Matthew Bendall, Solaiappan Manimaran, Changjin Hong, Nathan L. Clement, Eduardo Castro-Nallar, Quinn Snell, G. Bruce Schaalje, Mark J. Clement, Keith A. Crandall, and W. Evan Johnson. Pathoscope: Species identification and strain attribution with unassembled sequencing data. Genome Research, 2013; DOI: 10.1101/gr.150151.112

Posted by Tim Sandle

Join discussion on quality control of microbial culture media

Hear Tim Sandle (microbiologist) and Liz Kerrigan (of ATCC) discuss the best practices relating to the quality control of microbiological culture media in a free and interactive webinar.

To find out more details, go to the American Pharmaceutical Review.

Posted by Tim Sandle

General Chapter 601 Aerosols: correction

The USP has issued the following notice: Correction to Pharmacopeial Forum 39(1): General Chapter 601 Aerosols, Nasal Sprays, Metered-Dose Inhalers, and Dry Powder Inhalers.

USP recently determined that there was an error in General Chapter <601> Aerosols, Nasal Sprays, Metered-Dose Inhalers, and Dry Powder Inhalers published in the Pharmacopeial Forum 39(1) [Jan.–Feb. 2013]. Section D.1 Calculations under D. Data Analysis should be marked for deletion.

The General Chapter has been replaced and the corrected version is now available.

Posted by Tim Sandle

Gut microbes used to treat immune diseases

An oral administration, consisting of a cocktail of bacteria derived from the human gut, seems to reduce colitis and allergy-invoked diarrhea in mice.

Do probiotics work? One scientific study seems to suggest that the administration of 'beneficial' bacteria can treat certain diseases. With the study, scientists have demonstrated that a blend of specially selected strains of Clostridium bacteria derived from humans can significantly reduce symptoms of certain immune disorders in mice.

Clostridia bacteria include the well-known tetanus and botulism toxins. For the study, the researchers used strains of Clostridium derived from a sample of human feces. The experiments involved taking germ-free mice, bred to have colitis and allergy-induced diarrhea. The mice were then treated with specially selected strains of human-derived Clostridia and the results appeared to be successful.

The reason for the success is because the bacteria appear to stimulate a type of immune cells called regulatory T cells. These cells produce important anti-inflammatory immune molecules.

Alexander Rudensky, an immunologist at the Memorial Sloan-Kettering Cancer Center in New York and a cofounder, of Vedanta Biosciences, is quoted by the website the Scientist as saying: "It’s very valuable to see studies like this one, where detailed analysis of microbial compositions is linked to biology." The success of the animal studies may well lead to future trials conducted on people.

The results of the study have been published in Nature in a paper titled 'Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota'.

Posted by Tim Sandle

Study to assess impact of new bacterial threat: ESBL E. coli

The U.K. government is launching a new study into the impact of a microorganism called Extended-spectrum beta-lactamase Escherichia coli (ESBL-positive E. coli) in order to help combat the spread of this antibiotic-resistant bacterial strain.

Escherichia coli is the most common pathogen of bacterial infections worldwide. It has been estimated that as many as 80% of urinary tract infections are caused by E. coli. E. coli infections can also cause infections in the intestine, with young children, older people and those with compromised immune systems at greatest risk of being affected by the bacteria.

One of the concerns in modern medicine is the development of antibiotic resistant bacteria, a phenomenon that has arisen partly to the widespread (or ‘overuse’) of antibiotics. There are several bacteria strains of concerns (one of the most infamous being MRSA). Certain bacteria, like some strains of E. coli, can produce enzymes called extended-spectrum β-lactamases (ESBLs) that destroy, and confer resistance to, certain classes of commonly used antibiotics.

In order to assess the impact, research will be carried out by Public Health England and funded by the Department of Health to establish the most significant reservoirs of ESBL E. coli, looking at sewage, farm slurry and raw meat to assess potential risks to human health.

The research project will also look at stool samples from patients who have no symptoms of illness to see whether the bacteria are carried in their gut. The objective of the research is to gather data to help to reduce the numbers of infections, such as urinary tract infections or blood poisoning, that are caused by ESBL E. coli.

Discussing the project aims, Professor Neil Woodford, head of the antimicrobial resistance and healthcare-associated infections reference unit at Public Health England, is quoted on a government website as saying: "Its results will help to shape future intervention strategies to reduce the spread of these antibiotic-resistant strains of bacteria and to reduce the numbers of infections that they cause."

Posted by Tim Sandle

Farm workers carry high numbers of antibiotic resistant bacteria

Farm workers who work on farms where high levels of antibiotics are used in farm animals carry a high proportion of antibiotic resistant bacteria compared with farms that are antibiotic free.

The implication of this finding is that this is a further source of the spread of antibiotic resistant bacteria into the general community, which presents problems for the treatment of disease.

The reason for the issue coming to light stems from a study of industrial livestock workers in North Carolina. A range of swab samples were taken from the noses of different farm workers and then analyzed in a laboratory.

The farm workers who worked on farms where antibiotics are used carried far higher levels of antibiotic resistant bacteria, most notably methicillin-resistant Staphylococcus aureus (MRSA). MRSA is a strain of staphylococcus bacteria that is resistant to methicillin and certain first-line antibiotics called beta-lactams. The bacteria can cause serious infections of the skin, blood, lungs and bones. Infections with drug-resistant strains, like MRSA, can be particularly difficult to treat.

Many industrial livestock operations raise animals in large conferment buildings and use antibiotics, including non-therapeutically in animals' feed and water to promote their growth. Those concerned with the overuse of antibiotics and the resultant rise in antibiotic resistant bacteria have cautioned against such practices.

The study was a collaboration between Johns Hopkins Bloomberg School of Public Health, the University of North Carolina at Chapel Hill, the Rural Empowerment Association for Community Help, the George Washington University, and the Statens Serum Institute. The findings have been published in the journal PLOS ONE in a paper titled “Livestock-Associated Methicillin and Multidrug Resistant Staphylococcus aureus Is Present among Industrial, Not Antibiotic-Free Livestock Operation Workers in North Carolina.”

Posted by Tim Sandle

Is autism linked to gut bacteria?

New research suggests that the bacteria that reside in the human get influence children with autism spectrum disorder (ASD). This is related to stomach conditions in children who go onto show signs of autism.

The bacteria in the human gut and the way that the types and numbers change have been recently linked to a range of conditions, from digestion, fine-tuning body weight, regulating immune response, and producing neurotransmitters that affect brain and behavior. New revelations come as knowledge of the ‘human microbiome’ (the totality of microorganisms on an in the human body) increases. The latest connection is with gut bacteria and autism.

Autism is a disorder of neural development characterized by impaired social interaction and verbal and non-verbal communication, and by restricted, repetitive or stereotyped behaviour. Autism is defined as a spectrum disorder, due to the broad range of symptoms involved and the influence of both genetic and environmental factors.

The new research has shown that autistic children have a tendency to experience gastro-intestinal problems that can last into adulthood. This indicates a possible link with the types of gut bacteria and autism. Specifically, children with autism had significantly fewer types of gut bacteria, probably making them more vulnerable to pathogenic bacteria.

The researchers hope that the technique developed to show the link will become a diagnostic tool to pinpoint autism and also work as a guide to developing effective treatments for ASD-associated gut bacterial problems.

The research was carried out at the Arizona State University's Biodesign Institute. The findings have been published in the journal PLOS ONE in a paper titled “Reduced Incidence of Prevotella and Other Fermenters in Intestinal Microflora of Autistic Children.”

The report follows on from an earlier Digital Journal account of research which indicated that researchers have put forward a method for predicting autism in infants by examining how their brain reacts as they attempt to speak and process language.

Posted by Tim Sandle

Bacteria communicate to help resist antibiotics

New research from Western University unravels a novel means of communication that allows bacteria such as Burkholderia cenocepacia (B. cenocepacia) to resist antibiotic treatment. B. cenocepacia is an environmental bacterium that causes devastating infections in patients with cystic fibrosis (CF) or with compromised immune systems.

Research has shown that the more antibiotic resistant cells within a bacterial population produce and share small molecules with less resistant cells, making them more resistant to antibiotic killing. Therefore one mechanism of antimicrobial resistance appears to be based on chemical communication among bacterial cells.

For further details, see the following research paper:

Omar M. El-Halfawy, Miguel A. Valvano. Chemical Communication of Antibiotic Resistance by a Highly Resistant Subpopulation of Bacterial Cells. PLoS ONE, 2013; 8 (7): e68874

Posted by Tim Sandle