Friday, 31 August 2018

Monograph for Water, highly purified (1927) to be suppressed

Following a decision taken by the European Pharmacopoeia (Ph. Eur.) Commission at its 160th session (March 2018), the monograph for Water, highly purified (HPW) will be suppressed on 1 April 2019 from the Ph. Eur.

The monograph suppression is a consequence of the recent revision of the monograph for Water for injections (0169), which now allows for purification processes equivalent to distillation for producing water for injections (WFI), in addition to distillation. Hence, the HPW monograph is a duplication of the WFI monograph in terms of quality requirements and production methods, and as such became redundant.

Source: EDQM

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Thursday, 30 August 2018

New regulatory checkpoint in bacterial gene expression

According to the WHO, around 700,000 people die every year as a result of antibiotic resistance. In Germany, around 6,000 people die every year because treatment with antibiotics is not effective. Scientists at Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and the University of Oxford have now discovered that there is a point in the production process of the proteins at which it can be regulated by bacteria. This could be used as a starting point for the development of new antibiotics and help overcome resistance to antibiotics.

Antibiotics are used in the treatment of bacterial infections. They kill and inhibit the growth of bacteria, allowing the infection to subside and the patient to recover. However, during the last few years, increasing numbers of bacteria have developed so-called antibiotic resistance, which means they are resistant to the effects of antibiotics. Over time, these types of medication become ineffective and multi-resistant bacteria become even more widespread as a result.

In bacteria, the RNA is produced using a large protein complex called RNA polymerase (RNAP). The RNAP reads the DNA sequence and builds a copy of the RNA by joining nucleotides together -- the fundamental building blocks of RNA -- during a process called transcription. Since this production of RNA is fundamental for the survival of the bacteria, it has already been the subject of intensive research and used as the starting point for developing antibiotics, for example for the treatment of tuberculosis. However, it remained unclear how the production of RNA is also regulated at the stage of early transcription when RNAP has just begun to join together the first few RNA building blocks. This was the subject of the research carried out by the team of scientists.

The researchers used high-end fluorescence microscopy, which allowed them to monitor individual RNAP molecules as they started to produce RNA. They discovered that the initial RNA synthesis is strongly regulated -- a certain sequence of DNA forces the RNAP to pause for several seconds. It can only continue with RNA production after this pause.

This discovery completely changes our previous understanding of initial RNA synthesis in bacteria.


David Dulin, David L. V. Bauer, Anssi M. Malinen, Jacob J. W. Bakermans, Martin Kaller, Zakia Morichaud, Ivan Petushkov, Martin Depken, Konstantin Brodolin, Andrey Kulbachinskiy, Achillefs N. Kapanidis. Pausing controls branching between productive and non-productive pathways during initial transcription in bacteriaNature Communications, 2018; 9 (1) DOI: 10.1038/s41467-018-03902-9

Posted by Dr. Tim Sandle

Wednesday, 29 August 2018

1st International Mycoplasma qPCR Testing User Day

1st International Mycoplasma qPCR Testing User Day - PharmaLab Pre-Conference Event

Welcome to the 1st International Mycoplasma qPCR Testing User Day - PharmaLab Pre-Conference Event. We hope to provide a stimulating workshop of lectures and discussions with our keynote speakers. Please visit the agenda for detailed information here.

To sign up click on registration and follow the instructions.

Conference venue

Crowne Plaza (formerly Swissôtel) Düsseldorf / Neuss
Rheinallee 1
41460 Neuss
Tel.: +49 (0) 2131 77 - 00
Fax: +49 (0) 2131 77 - 1367

We are looking forward to your participation and to an exciting and informative event.

Please contact us with any questions.


For questions of content:

Dr. Bernd Simon
Marketing Manager Roche
CustomBiotech EMEA/LATAM
+49 621 759 8816

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

California Has Highest Number of Mosquito-Transmitted Disease Cases In U.S.

California leads the nation in mosquito-borne disease cases over the last decade, according to new data from the U.S. Centers for Disease Control and Prevention. The State reported 9,254 cases of mosquito-transmitted diseases between 2004 and 2016, followed by New York with 7,167 and Texas with 6,648. California had 100 times more mosquito-transmitted disease cases than Alaska (87), which reported the lowest number of cases in the country during the same period. The report included the total number of local and travel-associated disease transmission cases per state and did not adjust for population.

“These numbers are startling as they only represent mosquito-transmitted diseases that were reported to health officials said,” David Heft, president of the Mosquito and Vector Control Association of California. “Also not reflected in the data are the emerging disease threats the state faces due to the rise of invasive mosquitoes now present in 12 counties in Southern and Central California.”

Two invasive mosquito species, Aedes aegypti and Aedes albopictus, have been found in nearly 200 California cities and designated census areas since 2011 and they continue to spread throughout the state. Both invasive mosquito species are capable of transmitting viruses that are dangerous to people such as chikungunya, dengue, and Zika. Mosquitoes that are native to California are capable of infecting people with West Nile virus, which can cause debilitating cases of meningitis, encephalitis, and even death.

Vector control agencies have been working closely with public health officials to expand the toolbox of mosquito surveillance and control strategies. At the federal level, enhanced mosquito detection and suppression efforts have been funded by CDC Epidemiology and Laboratory Capacity (ELC) Grants. The grant funds have supported additional surveillance, control personnel, abatement equipment, community outreach, and education campaigns.

“It is critical that the federal ELC grant funds are secured and increased to support this vital public health work,” said Heft. “Specifically, we hope our legislators will pass the federal bill Strengthening Mosquito Abatement for Safety and Health Act, which is essential to maintaining and enhancing local resources to fight mosquitoes and mosquito-borne diseases.”

Mosquito control is a shared responsibility and National Mosquito Control Awareness Week, June 24-30, 2018, is an important way to raise awareness and educate residents about the public health threat mosquitoes pose to our communities. Residents are encouraged to integrate mosquito control into community events, support legislation to increase funding for mosquito control and prevention, and take preventative measures to minimize exposure to mosquito bites including:

1. Apply insect repellent containing EPA-registered active ingredients, including DEET, picaridin, oil of lemon eucalyptus, or IR3535 according to label instructions. Repellents keep mosquitoes from biting. DEET can be used safely on infants and children 2 months of age and older.

2. Dress in long sleeves and pants.

3. Install screens on windows and doors and keep them in good repair.

4. Eliminate all sources of standing water on your property, including in flower pots, old tires, and buckets.

5. Repair leaking faucets and broken sprinklers.

6. Clean rain gutters clogged with leaves.

7. Report neglected swimming pools and day-biting mosquitoes to your local mosquito and vector control agency.

For additional information on mosquitoes and mosquito-borne diseases visit the California Department of Public Health.

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Tuesday, 28 August 2018

Kitchen Towels Can be a Big Source of Bacteria in Your Kitchen

The kitchen is the heart of the home. You cook, eat and socialize in your kitchen; for many, it is the center of day-to-day living. The kitchen fuels bodies, minds and souls of families across the world, but it can also be the most veritable incubator for bacteria in the household. According to a study published by the University of Mauritius, and presented recently at the annual meeting of the American Society for Microbiology, your kitchen towels may be the leading culprit of pathogen advancement.

“Our study demonstrates that the family composition and hygienic practices in the kitchen affected the microbial load of kitchen towels,” said Dr. Biranjia-Hurdoyal. “We also found that diet, type of use and moist kitchen towels could be very important in promoting the growth of potential pathogens responsible for food poisoning,” she said.

Researchers collected a total of 100 kitchen towels after one month of use. Using standard biochemical tests, they concluded that 49% of the kitchen towels collected in the study had bacterial growth. The bacterial growth increased in number with family size—whether by extended family, or the presence of children.

Experts discourage using kitchen towels for multiple purposes (wiping utensils, drying hands, holding hot utensils, wiping/cleaning surfaces) because they had a higher bacterial count than single-use towels. They also warn against using humid towels because they too showed higher bacterial count than dry ones. Pathogens on kitchen towels would indicate that they could bear some responsibility for cross-contamination in the kitchen and, ultimately, food poisoning. Households with children, older adults or others with immunosuppression should be especially vigilant about hygiene in the kitchen. Your kitchen may be the busiest germ factory in your house, but by stepping up some basic hygiene, you can fight back against germs that tend to lurk around every corner in your kitchen.

Stop Foodborne Illness has 7 tips for keeping your kitchen as germ free as possible:
For towels/cloths hanging in the kitchen, allow them to dry after use.

  • Change out towels and cloths at least once a week.
  • Run kitchen towels and dish cloths through the washer at least once per week, using hot water.
  • Dry kitchen towels/cloths on high heat. After washing your hands properly , grab the hand towel, not the dish towel. Better yet, use a single-use paper towel.
  • Clean kitchen surfaces often (at least once a week), using disinfectant sprays or wipes.
  • Don’t get too attached to your sponges. Washing, drying or zapping sponges in the microwave can help reduce germs, but we suggest disposing of sponges at least once a week, or when they smell bad.
  • Keeping your kitchen germ-free can be challenging, but if your food safety practices include regularly sanitizing your kitchen, you can greatly reduce the risk of getting sick from potentially harmful pathogens. Many of our best memories are made gathered round the kitchen table – a place where everybody feels at home. We want everyone to get comfortable. Everyone, except foodborne pathogens.
About Stop Foodborne Illness

Stop Foodborne Illness is a national nonprofit public health organization dedicated to the prevention of illness and death from foodborne illness by promoting sound food safety policy and best practices, building public awareness, and assisting those impacted by foodborne illness. For more food safety tips please visit If you think you have been sickened from food, contact your local health professional.

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Monday, 27 August 2018

DuPont Nutrition & Health Microbiome Venture continues to strengthen its capabilities

Building upon the recently announced partnership with TFTAK in March 2018, the DuPont Nutrition & Health Microbiome Venture continues to strengthen its capabilities in announcing the third strategic research and development partnership. The newly forged relationship with INRA (French National Institute for Agricultural Research), through both the Micalis Institute and MetaGenoPolis, a pre-industrial demonstrator, will be focused on deciphering the molecular mechanisms of action of DuPont’s probiotic strains through a functional metagenomics approach.

INRA has developed and validated a high-throughput screening (HTS) platform to test the effect of large DNA fragment in genomic or metagenomic libraries on intestinal epithelial cell lines modified with reporter gene technology. This allows the screening of genomic and metagenomic clones on various reporter systems targeting pathways involved in homeostasis, metabolism, immune control as well as enteroendocrine cell activation.

Source and further reading: Microbiome Times

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Sunday, 26 August 2018

Probiotics Shown to Dramatically Improve IBS Gut Symptoms

Bio-Kult®, an award-winning, research-based probiotic, announces new clinical trial research confirming that the use of its multi-strain probiotic (14 different bacterial strains; 8 billion colony-forming units per day) is safe and superior to placebo in improving GI symptoms over a period of 4 months in patients with IBS-D (diarrhea-predominant irritable bowel syndrome).

In the largest-ever, double-blind randomized controlled trial (the gold standard for medical research) of probiotic supplements in IBS-diarrhea type patients ever conducted, dramatic improvements in symptoms were reported.

  • In the study of 360 patients who had IBS with diarrhea as their predominant symptom (IBS-D), those patients who took the probiotic supplement Bio-Kult® reported a 69 percent decrease in abdominal pain, compared to 47 percent in a group who took a placebo.
  • The four-month study conducted by the University of Bangabandhu Sheikh Mujib Medical University in Dhaka, Bangladesh also found that the number of patients who rated their symptoms as moderate to severe at the beginning of the study was reduced by 86 percent in the Bio-Kult® group, compared to 52 percent in those who took a placebo.
  • A total of 33.7 percent in the Bio-Kult® group reported that all their symptoms had disappeared at the end of the 16 weeks compared to just 12.8 percent in the placebo group.
In addition to relieving IBS-D symptoms, Bio-Kult® was also shown to markedly improve all aspects of Quality of Life (QoL) evaluated using as a 34-point IBS-QoL questionnaire. These included psychological issues such as anxiety about health, depression, lack of enjoyment of life, and feelings of having to avoid stressful situations.

Leading experts say the findings are a significant breakthrough in understanding the role bacteria play not only in physical gut symptoms but also psychological symptoms of IBS.

Dr. Philip Burnet, Associate Professor at Oxford University, a leading UK expert on the gut microbiome/ brain axis, says that although several symptoms within the IBS-QoL survey in the study were significantly improved after taking probiotic supplements, the reduction in dysphoria (unease or generalized dissatisfaction), and health worries were particularly noteworthy.

“The influence of gut bacteria on the brain is a topical area of research in neuroscience, and the microbiome-gut-brain-axis is considered a potential therapeutic pathway for brain disorders,” says Burnet. “Using probiotics that influence brain function, (also called ‘psychobiotics’), may, in the future, help alleviate conditions such as depression and anxiety.”

“There is a strong link between depression and IBS,” says Burnet, “and some researchers have suggested that mood disorders themselves may arise from a microbial imbalance within the body.”

Burnet cites another recent study by the University of Corki demonstrated that a single-strain probiotic, B.Longum, reduced depression scores in 22 IBS patients. “The Bio-Kult® formulation not only contains B.Longum, but also several other probiotic strains that have been reported to have psychotropic effects in both mouse models of anxiety and depressed mood, and in preliminary human studies,” says Burnet.

Study leader Professor Shamsuddin Ishaque said: “Over a period of 16 weeks Bio-Kult® produced statistically significant improvements in all key symptoms of IBD- D compared to placebo, including the severity and frequency of abdominal pain. The magnitude of these changes with Bio-Kult® was also very impressive.”

“IBS is a significant problem that decreases quality of life and places an enormous economic burden on healthcare systems globally. A safe and convenient IBS treatment that is capable of reducing pain by nearly 70%, not to mention completely resolving symptoms in more than a third of patients, demonstrates a profound benefit and holds great promise for this major medical concern,” says Dr. Ashton Harper, Head of Medical Affairs at Protexin Healthcare, makers of Bio-Kult.

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Saturday, 25 August 2018

Want to Know Where Lyme Disease is Most Severe?

One of the biggest challenges in gauging the spread of Lyme Disease in the United States has been the under-reporting of cases to health authorities. The Centers for Disease Control and Prevention (CDC) has reported that the numbers of Lyme disease cases actually reported from state and local health departments are probably much less than the actual number of cases. Lack of timeliness and localized reporting are also issues with some Lyme disease data.

The good news is that now, thanks to a simple website and app, users can tap actual diagnostic data from nearly one million doctors’ offices throughout the United States to get a clearer picture, literally, of where Lyme disease is most severe.

The Doctors Report™ Illness Tracker™ announced that its data shows 850,000 cases of Lyme disease were diagnosed across the U.S. in 2017, which is many times more than other available information. While it’s too early to tell where 2018 will fit in the pattern, the one thing anyone can do is check the Doctors Report ™ Illness Tracker™ to find out where and how severe Lyme disease is in their area right now.

The data is reliable because it’s based on actual diagnostic data, which Doctors Report collects from a national database from nearly one million doctors’ offices consisting of actual doctor-diagnosed and reported cases. Illnesses are ranked according to severity levels on a scale of 1 to 10 (10 being most prevalent).

“If you want to find out how severe Lyme disease is this week among children in your neighborhood, our app can tell you in seconds,” said Dan Shaw, the creator of Doctors Report. “While our algorithms are proprietary, and all personal information is stripped from the data to ensure it’s HIPAA-safe, the beauty of it is its simplicity. If you go to a doctor and are diagnosed with Lyme disease, the diagnosis without personal information, is responsibly and immediately used to tell us just where Lyme disease is spreading and how severe. We are the only people doing this.”’s national database of doctor-diagnosed Lyme disease represents just one of 15 illness tracked. The website and mobile app tracks illnesses nationally and locally to the zip code. It is current to within a week or so. And the data can be broken down across all age groups.

About the Doctors Report Website and App

Doctors Report is a website and app, powered by data from almost one million doctors’ offices nationwide. The data from doctors’ offices is cycled automatically so that it is the most current available anywhere. Doctors Report tracks 15 major disease and condition categories. Additional health risk categories will be added. The geographic accuracy of the data can be narrowed to zip code and broken down by health condition and age group. 

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Friday, 24 August 2018

Microbiome differences between urban and rural populations

An analysis comparing the intestinal microbiomes of both infants and adults living in rural and urban areas of Nigeria has revealed that not only are there many differences in adults living in subsistence environments versus urban ones but also that these variations begin at a very young age. The study appears June 5 in the journal Cell Reports.

Source: Cell Press

“We’ve always assumed that the microbiomes of infants were the same everywhere, and that differences came later in life,” says senior author Silvia Turroni of the Department of Pharmacy and Biotechnology at the University of Bologna in Italy. “We were surprised to find that the microbiomes of infants living in rural areas were missing components that we have long believed were standard to all infant populations–especially that they were essentially devoid of Bifidobacterium.” Bifidobacterium dominates the microbiomes of Western infants and has been considered a key element to healthy growth and development.

Previous studies that have analyzed the microbiomes of rural, hunter-gatherer societies have generally compared them to distant urban populations in Europe or the United States. This study was unique in that it looked at rural and urban African people in the same geographic area. Urban populations in the study were drawn from four state capital cities in Nigeria and the national capital, Abuja.

“This research was specifically designed to fill in gaps of knowledge about the variation of the human gut microbiome, as well as the metabolome, in relation to subsistence patterns in geographically close populations,” says first author Funmilola Ayeni of the Department of Pharmaceutical Microbiology at the University of Ibadan in Nigeria.

This study was also unique because it looked at both infant and adult microbiomes. For the purposes of this study, infants were defined as children up to age three. Unexpectedly, the investigators found that infants living in rural areas had microbiome profiles that were overall more diverse and more like those of adults.

The rural people included in the study, an agricultural society called the Bassa, consume a diet consisting of tubers, grains, and leafy soups, as well as untreated water. The urban diet contained processed foods and treated water but had more elements of a traditional Nigerian diet than what is seen in Western countries. Rural infants were given foods other than breast milk at a younger age than urban infants were.

Although it is only one factor, diet is an important component affecting the makeup of the intestinal microbiota. The researchers found that the rural population had a higher level of certain bacterial species that are important for digesting fiber. In addition, when metabolites in the samples were analyzed, rural populations had lower levels of amino acids and biogenic amines, suggesting a lower consumption of protein.

There were some drawbacks to the study. For one, the Bassa people usually don’t know their exact ages. Also, data about gender were not collected for the Bassa who participated, so the researchers were not able to look at whether there were differences between the sexes.

Still, the findings were notable. “Studies like these have profound evolutionary relevance because they recall ways of life that have characterized human history, from the hunting and gathering of our Paleolithic ancestors to small-scale agriculture, to the postindustrial Western lifestyle,” Turroni says.

“The distinctive microbial and metabolic traits observed in traditional populations, which tend to have much lower rates of Western diseases, could help us understand the mechanisms that lead to the rupture of these microbiome-host relationships,” Ayeni adds. “This could also potentially result in a greater understanding of the inflammation and immune dysregulation that follows.”

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Thursday, 23 August 2018

Parent cleansing paramount prior to skin-to-skin care

Neonatal intensive care units increasingly encourage meaningful touch and skin-to-skin care – aka “kangaroo care” – between parents and premature babies to aid the babies’ development. But a Michigan children’s hospital practicing skin-to-skin care noticed an unwanted side effect in 2016 – a spike in Staphylococcus aureus (SA) infections among newborns.

Hospital staff hypothesized that the two events were connected and implemented a three-part intervention in the small-baby unit that effectively reduced SA infections, according to new research presented at the 45th Annual Conference of the Association for Professionals in Infection Control and Epidemiology (APIC).

The three interventions introduced to curb SA infections were: increased awareness of hand hygiene, mandatory education of staff around SA, and the implementation of parent skin cleansing prior to skin-to-skin care.

In the first-year post-interventions, 20 babies in the small-baby unit developed SA infections, compared to 59 patients in the year prior.

“We know that skin-to-skin care and meaningful touch are good for the baby, but the increase in infections showed how this type of care giving can carry a risk,” said Gwen Westerling, BSN, RN, CIC, the study’s lead author and infection preventionist at Spectrum Health Helen DeVos Children’s Hospital. “The results demonstrate that interventions even as simple as cleaning the skin prior to care can drastically improve infection rates.”

Education about SA was also a critical component of this strategy. Following the intervention, 98 percent of staff surveyed knew of the requirements for parental skin cleansing. The mandatory staff education was conducted online. Leadership rounding reinforced the educational content and new cleaning requirements. In turn, nurses educated parents and family about the importance of cleansing before engaging in skin-to-skin care.

“Infection preventionists are uniquely attuned to the impact that process changes may have on the risk of infection,” said 2018 APIC President Janet Haas, PhD, RN, CIC, FSHEA, FAPIC. “Increased education around hand hygiene and cleaning procedures may seem straightforward, but we see again and again that they are key components in the reduction of healthcare-associated infections.”

Posted by Dr. Tim Sandle

Wednesday, 22 August 2018

ISO 14644 - The Revised Standard and Implications for Cleanrooms (webinar)

The international standard for cleanrooms has undergone a major revision. This webinar discusses the revisions in the context of global GMPs and the overall contamination control strategy. The webinar discusses testing approaches and the assessment of test data. The learning point is with keeping cleanrooms compliant.

New webinar - Date: Thursday, 30 August 2018 | Time: 10:00 AM PDT, 01:00 PM EDT | Duration: 60 Minutes

  • How to assess a cleanroom as built, at rest and in operation
  • How cleanroom standards inter-link to global GMPs
  • How to evaluate cleanroom data
  • How to assess cleanroom contractors
  • The importance of a risk based approach
  • Assessing microbial and particulate risks
This presentation will review the changes to ISO 14644 Parts 1 and 2 and will focus on the factors to consider when performing your risk assessment and creating your monitoring plan. How do justify sampling locations for classification? How often are you going to perform period reclassification? What about the other ancillary cleanroom testing required in ISO 14644-3? How often will you perform that based on risk? What items should you include in your monitoring plan document? Changes to these ISO standards will impact the way you perform cleanroom classification activities. Everything you need to know to be compliant to the changes.

See: Online Compliance Panel (

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Tuesday, 21 August 2018

Secret to longevity is in the microbiome and the gut

Science now tells us that we are what the bacteria living in our intestinal tract eat and this could have an influence on how well we age. Building on this, McGill University scientists fed fruit flies with a combination of probiotics and an herbal supplement called Triphala that was able to prolong the flies’ longevity by 60 % and protect them against chronic diseases associated with aging.

From Microbiome News

The study, published in Scientific Reports, adds to a growing body of evidence of the influence that gut bacteria can have on health. The researchers incorporated a symbiotic – made of probiotics with a polyphenol-rich supplement – into the diet of fruit flies.

The flies fed with the synbiotic lived up to 66 days old – 26 days more than the ones without the supplement. They also showed reduced traits of aging, such as mounting insulin resistance, inflammation and oxidative stress.

“Probiotics dramatically change the architecture of the gut microbiota, not only in its composition but also in respect to how the foods that we eat are metabolized,” says Satya Prakash, professor of biomedical engineering in McGill’s Faculty of Medicine and senior author of the study. “This allows a single probiotic formulation to simultaneously act on several biochemical signaling pathways to elicit broad beneficial physiological effects, and explains why the single formulation we present in this paper has such a dramatic effect on so many different markers”.

The fruit fly is remarkably similar to mammals with about 70 % similarity in terms of their biochemical pathways, making it a good indicator of what would happen in humans, adds Prakash.

“The effects in humans would likely not be as dramatic, but our results definitely suggest that a diet specifically incorporating Triphala along with these probiotics will promote a long and healthy life.”

The authors also say that the findings can be explained by the “gut-brain axis,” a bidirectional communication system between microorganisms residing in the gastrointestinal tract – the microbiota – and the brain. In the past few years, studies have shown the gut-brain axis to be involved in neuropathological changes and a variety of conditions such as irritable bowel syndrome, neurodegeneration and even depression. Few studies, however, have successfully designed gut microbiota-modulating therapeutics having effects as potent or broad as the formulation presented in the new study.

The herbal supplement used in the study, Triphala, is a formulation made from amalaki, bibhitaki and haritaki, fruits used as medicinal plants in Ayurveda, a form of traditional Indian medicine.

Susan Westfall, a former PhD student at McGill and lead author of the study, says the idea of combining Triphala and probiotics comes from her long-standing interest in studying natural products derived from traditional Indian medicine and their impact on neurodegenerative diseases.

“At the onset of this study, we were hopeful that combining Triphala with probiotics would be at least a little better than their individual components in terms of physiological benefit, but we did not imagine how successful this formulation would be,” says Westfall, who is now a postdoctoral fellow at the Icahn School of Medicine at Mount Sinai in New York, USA.

The new study, which includes data filed in a US provisional patent through a company cofounded by the authors, has the potential to impact the field of the microbiome, probiotics and human health.

Considering the broad physiological effects of this formulation shown in the fruit fly, Prakash hopes their formulation could have interesting applications in a number of human disorders such as diabetes, obesity, neurodegeneration, chronic inflammation, depression, irritable bowel syndrome and even cancer.

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Monday, 20 August 2018

Why Bacteria Survive in Space

In professor George Fox’s lab at the University of Houston, scientists are studying Earth germs that could be contaminating other planets. Despite extreme decontamination efforts, bacterial spores from Earth still manage to find their way into outer space aboard spacecraft. Fox and his team are examining how and why some spores elude decontamination. Their research is published in “BMC Microbiology.”

To gain access into the uber-sanitized clean rooms at NASA’s Goddard Space Flight Center in Greenbelt, Maryland, the world’s largest clean room, or the Jet Propulsion Laboratory in Caltech, California, employees pass through a series of lobbies. One, with adhesive floor mats, traps dirt carried on shoes. Another, about the size of an old phone booth, delivers a forced-air shower where dozens of air jets blow away dirt and debris. Only after these sterilization measures can they don the bodysuits, head covers and other disinfected regalia.

And still, bacteria survive and have been carried onboard the International Space Station and found on the Mars Rover. The ability of bacteria to survive extreme conditions could potentially lead to a process called ‘forward contamination.’

“The search for life elsewhere is impacted by the possible transport of organisms from Earth to solar system bodies of interest,” said Fox, Moores Professor of Biology and Biochemistry and Chemical and Biomolecular Engineering at UH. Fox is no stranger to microbiology. In the 1970’s, along with fellow scientist Carl Woese, he revolutionized the field by discovering that archaea are a separate domain of life.

As with natural selection, the cleaning process inside clean rooms will eventually kill off the weaker bacteria while a stronger strain adapts and is unphased by the cleansers.

“No matter what we do, some bacterial spores appear to be finding ways to escape decontamination,” said Madhan Tirumalai, a post-doctoral biologist in Fox’s lab. “I’m trying to understand what makes these spores so special at their genomic level and relate these features with their ability to evade decontamination measures.”

It starts with sequencing

The Fox team studied non-pathogenic (non-disease-causing) bacteria that belong to the genus Bacillus and produce highly resistant spores. They were isolated from cleanrooms and spacecraft assembly facilities at the Jet Propulsion Laboratory.

They sequenced the complete genome of two strains resistant to peroxide and radiation: B. safensis FO-36bT and B. pumilus SAFR-032. Then they compared the genomes of those strains and that of another strain, B. safensis JPL-MERTA-8-2, with bacteria known to produce spores that are vulnerable to peroxide and radiation, such as the strain B. pumilus ATCC7061T. The B. safensis JPL-MERTA-8-2 strain was isolated from the Mars Odyssey Spacecraft and associated facilities at the Jet Propulsion Laboratory and later also found on the Mars Explorer Rover (MER) before its launch in 2004.

“The genome blueprint gave us the basic clues of what the organism might be harboring,” said Tirumalai. By comparing the blueprints of the four strains, they found 10 genes that are unique to the FO-36b, that are not found in any other organisms (including other Bacillus strains). That is 10 genes whose functions are unknown – or 10 suspects for why spores of B. safensis FO-36bT are resistant to peroxide and radiation, although it is not immediately obvious that the presence or absence of any specific gene or combination of genes is responsible for the variations in resistance seen.

“It is quite possible that distinctions in gene regulation can alter the expression levels of key proteins thereby changing the organism’s resistance properties without gain or loss of a particular gene. These are potential genes of interest with respect to the resistance of the spores of this strain” said Tirumalai.

As it turns out, four of these genes are found on phage elements of the bacterial strain. Phage, short for bacteriophage, is a virus that infects bacteria. Phages are major facilitators for transferring genes between microbes.

"The task to eliminate microbes in clean rooms, where spacecraft are assembled, or aboard spacecraft, will continue to be a challenge for NASA and other space agencies," said Tirumalai.

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Sunday, 19 August 2018

Distribution of biocide resistant genes and biocides susceptibility in multidrug-resistant bacteria

A new research paper of interest:


The aim of this study was to determine the frequency of biocide resistant genes, qacA, qacE and cepA in multidrug resistant (MDR) bacteria: Klebsiella pneumoniae, Pseudomonas aeruginosa and Acinetobacter baumannii and to correlate the presence or absence of resistant genes with biocides susceptibility. 

Materials and methods:

The study included 44 MDR K. pneumoniae, P. aeruginosa and A. baumannii microorganisms. The bacteria were screened for the presence of biocide resistant genes by the polymerase chain reaction (PCR) method. The test organisms were isolated from various clinical specimens in the Qassim region, Saudi Arabia. The in vitro susceptibility tests of the three biocides (benzalkonium chloride, cetrimide and chlorhexidine gluconate) were studied against the test isolates by broth microdilution method following Clinical and Laboratory Standards Institute guidelines. 


With the distribution of biocide resistant genes in K. pneumoniae, all 9 isolates (100%) possessed cepA; 4 (44.4%) and 1 (11.1%) isolate contained qacA and qacE genes respectively. Among 24 isolates of A. baumannii tested, cepA, qacA and qacE genes were found in 54.2%, 16.7% and 33.3% of isolates respectively. Among 11 P. aeruginosa isolates, 63.6% contained cepA gene, 18.2% contained qacE genes, and none of the isolates harboured qacA gene. There was no significant correlation between presence or absence of biocide resistant genes and high MIC values of the test isolates (p ≥ 0.2). 


Our observations imply that there was no significant correlation between presence or absence of biocide resistant genes and MICs observed in MDR K. pneumoniae, P. aeruginosa and A. baumannii. Further studies are required to find to confirm the trend of reduced susceptibility to biocides of problematic nosocomial pathogens.


Vijayakumara, R., Sandle, T., Al-Aboodya, M. S., AlFonaisana, M.K., Alturaikia, W., Mickymaraya, S., Premanathana, M., Alsagabya, S.A. (2018) Distribution of biocide resistant genes and biocides susceptibility in multidrug-resistant Klebsiella pneumoniae, Pseudomonas aeruginosa and Acinetobacter baumannii — A first report from the Kingdom of Saudi Arabia, Journal of Infection and Public Health, online:

To access see: Research Gate

Posted by Dr. Tim Sandle

Saturday, 18 August 2018

Deep biosphere microbes expand the chemical signatures of life

Search for signs of ancient microbial life in the geological record is challenging due to degradation of the primary organic material. Therefore, proof of biogenic origin often relies on chemical signatures that microorganisms leave behind. A new study of minerals in rock cracks presents chemical signatures that are definite proofs of widespread ancient life processes in the energy-poor continental crust. More importantly, the study greatly expands the known chemical variation of sulfur, one of the key elements in microbial metabolisms. This gives new clues to what type of chemical signatures to expect from life in extreme environments, including search for life on other planets.
A major part of the biologic activity on Earth is hidden underneath the soil down to depths of several kilometres in an environment coined the “deep biosphere”. Studies of life-forms in this dark anoxic system have implications for how life has evolved under conditions we consider extreme. It also gives clue to how life may have evolved on other planets where hostile conditions inhibit colonization of the surface environment. The knowledge about ancient life in this environment deep under our feet is still extremely scarce.

Search for signs of ancient life on Earth in the geological record is often challenging because the primary organic material has been partially or completely degraded. In these situations, the proof of biogenic origin relies on geochemical signatures that microorganisms leave behind, or to morphological shapes of mineralized microbial remnants. In search for life on other planets, such as on Mars, the same challenges can be expected and it is therefore important to know what type of chemical signatures to expect from life in extreme environments.

In numerous cracks down to depths of 1700 meter that have been partly sealed by crystals grown in them, a team of researchers led by Dr. Henrik Drake from Linnaeus University, Sweden, has traced ancient microbial processes, dominantly focusing on microbes that transform sulfate to sulfide in their metabolism. The multi-disciplinary approach included micro-scale measurement and imaging of sulfur coupled with geochronology within minerals formed in response to microbial activity at several Swedish granitic rock sites. This is the most extensive study of this process in the continental crust yet and the findings suggest that the process has been widespread in time and space in the bedrock.

Henrik Drake explains how they tapped the chemical archive of minerals to decipher ancient microbial processes:

“It is well known from other environments that when microorganisms use sulfate in their metabolism they produce minerals that have characteristic sulfur composition. In fact, relative abundance of different sulfur atoms (isotopes) is among the most widely used geochemical tools to trace microbial processes in the geological record. Our micro-analyses within crystals of the sulfide mineral pyrite showed the most extreme sulfur isotope composition ever recorded on Earth.”

“These signatures are definite proofs of ancient life processes in the continental crust, but more importantly they greatly expand the known isotope variation of sulfide minerals produced following microbial metabolisms. In more detail, the span of the ratio of sulfur isotopes 34S to 32S was as large as -54 to +132 per mil (normalized to the CDT standard). Adaptation to energy poor conditions, slow metabolism and complete exhaustion of the available dissolved sulfate as it moved through the fracture system are explanations for the exceptional values.”

Christine Heim of University of Göttingen, Germany, a co-author of the study, says:

“In addition to the isotope signatures we found biomarkers of ancient organic remains of surficial origin (e.g. land plants) preserved within the mineral coatings at great depth. A connection to the surface biosphere is thereby evident and may explain why the marks of microbial activity abruptly disappear at around 1000 m depth.”

Direct timing constraints facilitated by newly developed dating techniques revealed when the biologic activities started - at 360-400 Million years ago. Deep life in the energy-poor continental crust has evidently thrived over eons, which is relevant information when searching for life in similar subsurface settings of other planets. Henrik Drake summarizes:

“Our multi-method approach has made us aware that biological signatures in extreme environments can be different from what we expected earlier, and would thus be very suitable for investigation of extra-terrestrial environments.”

Co-author Martin Whitehouse of The Swedish Museum of Natural History adds:

“The ability to rapidly measure sulfur isotopes at high spatial resolution by ion microprobe permits a better appreciation of both the range and distribution within single pyrite crystals. It is intriguing that our previous studies of the same fracture system found the most variable carbon isotope compositions in carbonate minerals yet recorded on Earth. We can therefore conclude that our exploration of ancient life in cracks of terrestrial magmatic rocks will change the way we look at geochemical proxies for microbial activity in extreme environments.”

The results are presented in the article “Unprecedented 34S-enrichment of pyrite formed following microbial sulfate reduction in fractured crystalline rocks” in the journal Geobiology (published online June 26, 2018).

Posted by Dr. Tim Sandle

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