Citizen science project for the human microbiome

uBiome is a citizen science project that allows the public access to cutting edge sequencing technology to understand their health through the microbiome.

The service allows users to send in body samples and their microbial flora can be characterised. The project is part of an activity to build up a database of the diversity of microorganisms carried in and on the human body. Various studies have linked the diversity microorganisms to human health.

According to uBiome, “Five Things Your Microbiome Can Tell You” are:

1. Obesity.  Ley et al (2006) and others have identified gut microbes associated with obesity, such as Eubacterium rectale. In addition, Upadhyay et al (2012) did experiments with mouse models and suggested the possibility that the microbiome could be manipulated for weight control in the near future

2. Dietary composition. Wu et al (2011) found that gut enterotypes were strongly associated with long-term diets, particularly protein and animal fat (Bacteroides) versus carbohydrates (Prevotella).

3. Antibiotics.  If you have recently taken antibiotics, your gut microflora may not yet have been replenished. Dethlefsen et al (2008) found that ciprofloxacin treatment influenced the abundance of about a third of the bacterial taxa in the gut. Similarly, Jernberg et al (2007) found that long after the selection pressure from a short antibiotic exposure has been removed, there are persistent long term impacts on the human intestinal microbiota that remain for up to two years post-treatment.

4. Allergies. Is your nasal microbiome associated with the profile of chronic sinusitis? Abreu et al (2012) found that multiple, phylogenetically distinct lactic acid bacteria were depleted concomitant with an increase in the relative abundance of a single species, Corynebacterium tuberculostearicum, in patients suffering from chronic sinusitis.

5. Bacterial vaginosis. If you have a penis, your microbiome may be correlated with bacterial vaginosis in women. Price et al (2010) found that two families found in certain penis microbiomes -- Clostridiales Family XI and Prevotellaceae -- have been previously associated with bacterial vaginosis. This may correspond to frequent infections in your partner.

The results of the study are made public (unless the user opts out), with the aim of advancing scientific understanding.

Please note, this is not a free service and it is not endorsed by this website.

For details, see uBiome

Posted by Tim Sandle

The microbial diversity in the middle and upper troposphere

Researchers have used genomic techniques to document the presence of significant numbers of microorganisms, principally bacteria, in the middle and upper troposphere, that section of the atmosphere approximately four to six miles above Earth's surface.

Whether the microorganisms inhabit this portion of the atmosphere (perhaps living on carbon compounds also found there) or whether they are lofted there from Earth's surface is not known.

The research was supported by NASA and the National Science Foundation, has been published online by the journal Proceedings of the National Academy of Sciences.

Natasha DeLeon-Rodriguez et al. Microbiome of the upper troposphere: Species composition and prevalence, effects of tropical storms, and atmospheric implications. PNAS, 2013

Posted by Tim Sandle

Blue light for treating bacterial infections

Blue light can selectively eradicate Pseudomonas aeruginosa infections of the skin and soft tissues, while preserving the outermost layer of skin, according to a new study published in the journal Antimicrobial Agents and Chemotherapy.

T. Dai, A. Gupta, Y.-Y. Huang, R. Yin, C. K. Murray, M. S. Vrahas, M. Sherwood, G. P. Tegos, M. R. Hamblin. Blue light rescues mice from potentially fatal Pseudomonas aeruginosa burn infection: efficacy, safety, and mechanism of action. Antimicrobial Agents and Chemotherapy, 2012

Posted by Tim Sandle

Drinking water is rich in microbial life

Flow cytometry (FCM) studies have been used for the quantification of microbial cells in drinking water. A recent study has shown that drinking water contains100 to 10,000 times more living cells than the conventional plate count method would suggest.

The microbial content of water is normally assessed using the heterotrophic plate count (HPC). The HPC method involves growing any bacteria present in a sample of water onto solid nutrient media (incubated at a warm temperature), and the colonies formed are then counted.

The weakness with the HPC method are the incubation time and the fact that only a fraction of the living cells actually present in samples are counted (the so-termed ‘viable but non-culturable’ microorganisms).

The utilisation of FCM methodology can be used to determine, more accurately, the total cell count in a water sample within a matter of minutes.

FCM works by staining any cells contained in a sample with fluorescent dyes, which bind to DNA. The cells are then passed in single file through a glass capillary, where they are exposed to a beam of light from a laser. The resultant scatter and fluorescence signals are picked up by detectors, and analytical software is used to classify each individual particle (cell).

To read more about this technology and the associated research, visit EAWAG: Swiss Federal Institute of Aquatic Scienceand Technology.

Posted by Tim Sandle

Pharmig celebrates 20 years of microbiology forums

Celebrating its 20th year of existence Pharmig, the UK organisation for pharmaceutical microbiology professionals, got to grips with future regulatory challenges and technical issues. One of the speakers, Dr Tim Sandle, provides highlights from the event.

To read this special report about the microbiology conference, visit the Cleanroom Technology website

Posted by Tim Sandle

Pharmacopeia Forum Vol. 39 (2013)

A new edition of the Pharmacopeia Forum Vol. 39 No.1 Jan– Feb 2013 has been published. Among the items of interest for laboratory staff are:

Chapter 202 Identification of Fixed Oils by Thin-Layer Chromatography [NEW]

(Revision proposal target, USP37-NF32)

This new chapter proposes an orthogonal test to determine the identity of fixed oils. The procedure is harmonized with European Pharmacopoeia general chapter 2.3.2. Identification of Fatty Oils by Thin-Layer Chromatography

Chapter 231 Heavy Metals

(Revision proposal target, USP37-NF32)

To improve and harmonize monographs and general chapters, the USP proposes to omit Heavy Metals chapter 231 and all references to this general chapter from USP–NF monographs and other general chapters. USP is replacing <231> with two new general chapters on elemental impurities:

Chapter 232 Elemental Impurities—Limits

Chapter 233 Elemental Impurities—Procedures

These two chapters were published in the Second Supplement to USP 35–NF 30

Chapter 853 Flourescence Spectroscopy [NEW]

(Revision proposal target, USP37-NF32)

Spectrophotometry and Light–Scattering <851> will be replaced by a family of chapters pertaining to atomic absorption, UV–Vis, infrared, and fluorescence spectroscopy methods. Each of these chapters will be presented in pairs (one numbered below 1000 and one numbered above 1000). Chapter <853> is based on application of the method when applied to a procedure in a monograph. Its sections are Introduction, Instrument Qualification, Procedure, and Validation and Verification

Chapter 1853 Flourescence Spectroscopy – Theory and practice [NEW]

(Revision proposal target, USP37-NF32)

The general information chapter describes theory and instrumentation used to support development of a compendial procedure. That chapter's sections are Theory, Instrumentation, Factors That Affect Quantitation, Calibration of Fluorescence Instruments, and Procedure Validation

GI Tract bacteria protect against autoimmune disease

Early life exposure to normal bacteria of the GI tract (gut microbes) protects against autoimmune disease in mice, according to research published on-line in the January 17 edition of Science.

The authors of the paper state that the findings support the so-called 'hygiene hypothesis,' which suggests that the dramatic increase in autoimmune and inflammatory diseases over the past 50 years results from changes in our exposure to microbes.

The reference is:

Janet G. M. Markle, Daniel N. Frank, Steven Mortin-Toth, Charles E. Robertson, Leah M. Feazel, Ulrike Rolle-Kampczyk, Martin von Bergen, Kathy D. McCoy, Andrew J. Macpherson, and Jayne S. Danska. Sex Differences in the Gut Microbiome Drive Hormone-Dependent Regulation of Autoimmunity. Science, January 17, 2013

Guidance for Industry and FDA Current Good Manufacturing Practice for Combination Products

The FDA have issued a new guidance document entitled ‘Guidance for Industry and FDA Current Good Manufacturing Practice for Combination Products’.

The brief for the document reads: “This document provides guidance to industry and FDA staff on the applicability of current good manufacturing practice provisions to combination products as defined under 21 CFR 3.2(e). Such provisions apply to the manufacture of combination products to ensure that the product is not adulterated; the product possesses adequate strength, quality, identity, and purity; and the product complies with performance standards as appropriate for the marketed combination product.”

For further details, see A3P

ISO 14698 revision process underway

The following article of interest has been posted by Cleanroom Technology.

Following a recent meeting, a decision has been taken by the international cleanroom community to move forward with the work to revise ISO 14698 – Cleanroom Biocontamination Control.

The standard will seek to establish control requirements such as the important environmental quality attributes. It will also refer to test methods and validation, including assessment of environmental monitoring equipment like air samplers. There will also be a section on data handling.

The main changes to ISO 14698 under discussion are:

• ·         A new classification system for viable counts, split into surface and air cleanliness,
• ·         Guidance for assessing cleanrooms at start-up or after modifications for bioburden, in a similar way that cleanrooms are currently assessed for particle counts,
• ·         Guidance on viable monitoring methods,
• ·         Recommendations for data analysis.

The vote was accepted with 13 countries giving ‘Yes’ votes and only the USA ANSI team voting ‘No’.

The countries that voted a ‘Yes’ in support of this work were Brazil (ABNT), Germany (DIN), China (SAC), France (AFNOR), Japan (JISC), Sweden (SIS), Italy (UNI), Korea, Republic of (KATS), Ireland (NSAI), Switzerland (SNV), Netherlands (NEN), Denmark (DS), UK (BSI). Twelve of the countries are putting forward experts to take part (Korea is not sending an expert).

The US team has stated it will no longer be putting forward an expert for the ongoing work on this document.

The standard is seen by some in the US as adding unnecessary cost to industry. In addition the US Pharmacopoeia Chapter <1116> "Microbiological Evaluation of Clean Rooms and Other Controlled Environments”, which has only recently been updated, would possibly be at variance with some of the resulting ISO revisions.

Speaking about the potential revisions, Tim Sandle, Head of Microbiology, BPL, considers that one aim of the revised standard – to have a viable classification approach for cleanrooms – requires further discussion. “Cleanrooms are clean if verified by their physical parameters and remain so provided people do not enter them. The current thinking of orientating monitoring locations and frequencies towards risk seems a more sensible approach. Another aspect, to have an average count for a clean area on classification, stands in contrast to the current USP approach that looks at incident rates.”

Source: CleanroomTechnology 

EU GMP draft chapters produced

On 17 January 2013, the EU Commission published the drafts of 4 revised chapters of the EU GMP Guide, according to the ECA.

The changes relate to:

• Chapter 3 ‘Premise and Equipment’. Paragraph 6 has been revised and extended. It contains regulations on how to avoid cross-contamination and the changes made are linked with the revised contents of Chapter 5 Production. See: Chapter 3
• Chapter 5 ‘Production’. Changes have been made to paragraphs 17 to 20, also in relation to cross-contamination. In addition, paragraphs 26 to 28 on Qualification of Suppliers have also been modified. See: Chapter 5
• Chapter 6 ‘Quality Control’. The chapter now provides new requirements on the transfer of analytical methods as well as new regulations about the handling of out-of-specification results.  See: Chapter 6
• Chapter 8 outlines the importance of a quality management system for the evaluation of quality defects in relation to product recalls and likewise clarifies the requirements regarding the reporting (when and how) of quality defects to the authority.  See: Chapter 8

For further details and links to the drafts, please see the ECA website.

What types of bacteria are found in hailstones?

Researchers have found a rich diversity of microbial life and chemicals in the ephemeral habitat of a storm cloud, according to a study published in the journal PLOS ONE by Tina Šantl Temkiv and colleagues from Aarhus University, Denmark.

The researchers found that found that storm clouds carried several species of bacteria typically found on plants and almost 3000 different compounds usually found in soil. However, the hailstones had very few soil-associated bacteria or chemicals that would usually occur in plants.

The article reference is:

Tina Šantl-Temkiv, Kai Finster, Thorsten Dittmar, Bjarne Munk Hansen, Runar Thyrhaug, Niels Woetmann Nielsen, Ulrich Gosewinkel Karlson. Hailstones: A Window into the Microbial and Chemical Inventory of a Storm Cloud. PLoS ONE, 2013; 8 (1)

It can be accessed here: PLOS One

Antibiotic resistance

An interesting article has been published in the New England Journal of Medicine. The article addresses the global problem of antibiotic resistance.

Antibiotic-resistant microbes infect more than 2 million Americans every year and kill more than 100,000 annually. At the same time, the development of new antibiotics to treat these infections is plummeting, leading to our call for entirely new approaches to the problem.

The authors call for novel approaches based on a "reconceptualization of the nature of resistance, disease and prevention."

Among their recommendations are stricter monitoring and controls for prescribing antibiotics and changes in hospital practices, including greater disinfection and less usage of invasive materials than can transmit antibiotic-resistant bacteria into the body.

The article reference is:

Brad Spellberg, John G. Bartlett, David N. Gilbert. The Future of Antibiotics and Resistance. New England Journal of Medicine, 2013; 368 (4): 299

It can be accessed here: NEJM