Category Archives: Physiology News

Articles pulled from our magazine, Physiology News.

The female athlete: A balancing act between success and health

By Jessica Piasecki, Manchester Metropolitan University, UK, @JessCoulson90

A longer version of this article originally appeared in Physiology News.

There is a very fine line between training, competition, and recovery for the elite athletes (1). For female athletes, they have an extra balance to take into consideration: the menstrual cycle.

The monthly cycles

The menstrual cycle is a natural process and is essential to maintain bone health and fertility. It can start from the age of 12 and continues until the onset of menopause around the age of 49-52.

The cycle occurs over a period of 28 days. The first 14 days are known as the follicular phase. During this phase, around day 10, the hormones oestrogen, LH (luteinizing hormone) and FSH (follicular stimulating hormone) rise, reaching their peak around day 14.

LH reaches a level double than that of both oestrogen and FSH. After day 14 LH levels rapidly drop off while oestrogen and FSH fall off more slowly, over a 5 day period. The second 14 days are known as the luteal phase and there is a gradual increase in another hormone, progesterone, which reaches a peak around day 22 and returns to base levels at day 28.


Bone stability and structure

Of these three hormones, oestrogen is a key regulator of bone resorption, without oestrogen there would be an excess of bone being broken down over new bone being formed. Bone is in a state of constant turnover, with the help of two types of bone cells (osteoblasts and osteoclasts). Osteoblasts are involved in bone formation, while osteoclasts are involved in bone resorption.

Bone resorption occurs at a much higher rate than formation; bone resorption takes just 30 days whereas the bone remodelling cycle takes 4 months. Therefore, a slight imbalance can lead to a bone fracture very quickly (2).

More is not always better

Elite female athletes, particularly those involved in sports that usually adopt a leaner physique with low body fat, are at a greater risk of disordered eating. The reasons for this disordered eating could be external pressures from teams, coaches and sponsors, or the athletes themselves having the belief that the leaner and lighter they are, the quicker they will be. These pressures may also cause the athlete to push their body to further extremes.


Without the necessary energy intake, the menstrual cycle will most likely become irregular and eventually cease (which is known as amenorrhea). Amenorrhea causes the levels of oestrogen to become reduced, leaving a disproportionate ratio of osteoblasts and osteoclasts, and a higher rate of bone resorption.

This may ultimately lead to bone injuries, (the precursor to osteoporosis), or even osteoporosis at a very young age, making any further career achievements even more difficult.

These three symptoms (disordered eating, amenorrhea and osteoporosis) became more prevalent in the 1990s and were termed ‘The Female Athlete Triad’ in 1997 by the American College of Sports Medicine. It has been estimated that only 50% of trained physicians are knowledgeable about the female athlete triad (3). More recently the triad has been regrouped within a term known as RED-S (Relative energy deficient syndrome); deemed to result from continual disordered eating. Being in a state of energy deficiency for a long duration can disrupt many processes within the body, including the cardiovascular, digestive and hormonal . Redefining the RED-S also allows male athletes who present with similar issues to be included (4).

Current research has looked at the differing effects of the components of the triad on injuries, and bone and muscle health. At Manchester Metropolitan University, we have carried out our own research on some of the UK’s most renowned female endurance runners, investigating the effects of altered menstrual cycle on bone health. Athletes with amenorrhea presented with a greater endocortical circumference (the outer circumference of the inner cortical bone in the tibia (lower leg) and radius (forearm) than controls. Only the athletes with regular menstrual cycles (eumenorrheic) had a greater cortical area, in the tibia and radius, compared to controls. The athletes with amenorrhea had thinner bones (i.e. larger but not denser). We are working to better understand the issues, so accurate diagnosis will become more frequent.

What we really need is education at a young age, as most athletes become familiar with the triad only once they have been diagnosed with a bone injury. If athletes are made aware of the symptoms and issues around the triad before they occur, then nutrition and menstrual cycles can be more closely monitored as they progress through their athletic careers.

Read the full-length version of this article in our magazine, Physiology News.


  1. Barnett, A (2006). Using recovery modalities between training sessions in elite athletes does it help? Sports Med (36), 781-96
  2. Agerbaek, M. O., Eriksen, E. F., Kragstrup, J., Mosekilde, L. and Melsen, F. (1991) A reconstruction of the remodelling cycle in normal human cortical iliac bone. Bone Miner, 12 (2), pp. 101-12.
  3. Curry, E, Logan, C, Ackerman, K, McInnia K, Matzkin, E (2015) Female athlete triad awareness among multispecialty Physicians. Sports Med Open. 1:38.
  4. Tenforde, AS, Parziale, A, Popp, K, Ackerman, K. (2017) Low Bone mineral density in male athletes is associated with bone stress injuries at anatomic sites with greater trabecular composition. Am J Sports Med. DOI: 10.1177/0363546517730584

Exercise, stress and Star Wars: Best of 2017 roundup

Happy New Year! In 2018, we look forward to more physiology fun, and to giving you an insight into the exciting new developments in the Science of Life!

Physio-what, you ask? Take a look at our animation below introducing physiology! Scroll down to find out more about a centuries-old shark patrolling the deep Arctic Ocean, how being active gives children’s hearts a head start for life, and why it’s time scientists took back control from exercise gurus, in our best of 2017 roundup!

1. Exercise scientists should fight the exercise gurus

Social media apps - With new Google logo

Exercise gurus build strong rapports with their audience to encourage commitment, but they will often simplify a large body of scientific evidence to back up their advice.

In this post, Gladys Onambele-Pearson and Kostas Tsintzas discuss the risks of letting exercise gurus disseminate exercise science to the public, and why it may be time for scientists to become the actual celebrities.

2. The Myth of a Sport Scientist


There is a mismatch between the perceptions and reality of what a sport scientist is and what skills this career entails: just because exercise scientists use models of sport performance, exercise bouts or physical activity sessions, doesn’t mean that there aren’t complex scientific skills, theories, analytics and techniques behind the work.

Read more from sport scientist Hannah Moir in this post.

3. Shark Diary, Episode I: On the trails of the Greenland shark


How do you keep lab chemicals cool when there’s no fridge in your room? Well, if you’re in chilly Denmark, you could just hang them outside your window.

Holly Shiels did just that in Copenhagen, on her way to Greenland to join a team of physiologists on a shark research mission. Their aim was to gather data on the physiology of the Greenland shark. Clarifying how these animals reach hundreds of years of age without developing diseases associated with human ageing, like cancer and heart disease, could lead to new therapies down the line, and understanding shark physiology is also important for their conservation.

Read more about the mission in this post, and check out watch below to see the researchers braving the icy waters of the North Atlantic and releasing a tagged Greenland shark.

4. Breath of the Sith: a case study on respiratory failure in a galaxy far, far away


Have you always wondered what actually is going on behind the mask? Darth Vader’s acute respiratory failure appears to be the consequence of a number of factors, including direct thermal injury to the airways, chemical damage to the lung parenchyma caused by inhalation of smoke and volcanic dust particles, carbon monoxide poisoning, as well as secondary effects to his severe third degree burns, which seems to cover ~100 % of his total body surface area.

Read on as Ronan Berg and Ronni Plovsing make a tongue-in-cheek diagnosis of the numerous respiratory ailments of everyone’s favourite Sith Lord.

5. Exercise now, thank yourself later


Exercise is good for the heart, but the benefits fade soon after we stop training… or so we thought. Studies so far have focused on adults, but research published last November in The Journal of Physiology reveals that exercise in early life could have lifelong benefits for heart health.

This is because young hearts are able to create new heart muscle cells in response to exercise, an ability that is mostly lost in adulthood. Glenn Wadley, Associate Professor at Deakin University and author of the study, explains the findings in this post, and makes the case for children to get active!

As if that wasn’t enough reason to exercise, being active is one of three tips that can help relieve the stress we feel for instance at the approach of exams. Watch our animation below to find out more about what stress does to our bodies, and start making good on those New Year resolutions!

Careers – no ‘one size fits all’ for scientists

A longer version of this article originally appeared in Physiology News.

‘What matters most is how well you walk through the fire’ – Charles Bukowski

The career path of scientists is oft the result of happenstance; a chance meeting at a conference, a quirk in a dataset, a change in personal circumstance. There’s no one size fits all for scientists’ careers. We sought to highlight this with several case studies to encourage you on your way.

The beauty of science is it takes you across borders
by Rebecca Dumbell, Postdoctoral Training Fellow, MRC Harwell Institute, UK

I completed my PhD from the Rowett Institute of Nutrition and Health, University of Aberdeen in 2014. The Rowett had merged with the University a few years before I joined, and combined with the rural location at the time, this meant that it still had the feel of a research institute. Towards the end of my PhD I heard about a postdoc position coming up at the University of Lübeck in Germany through word of mouth. In a bit of a whirlwind I flew out to Germany for my interview the day after submitting my thesis, and I started the job a few months later.

Getting set up in my new job and new country was a challenge. I quickly learned that I needed a lot of documents, all from different offices located very far from each other, and they all had to be collected in a particular order. My EU passport smoothed the process and made my experience much easier than what I witnessed my non-EU colleagues go through. Within 1 week I had everything I needed, including a place to live, a bank account, health insurance and a pension plan.


Lübeck. / Shutterstock

I spent almost 2 years as a postdoc in Lübeck and I really loved living in Germany. Half of my colleagues were German and the rest came from all over the world, all speaking English in the lab. This was a lot of fun and we set up things like ‘international cooking club’ and, my personal favourite, whisky club. I found that as the only native English speaker I was the go-to proofreader; this certainly improved my grammar if not the work I was checking!

I now work at the MRC Harwell Institute in Oxfordshire as a Postdoctoral Training Fellow, and again find myself in a research institute in a rural setting. This comes with its own advantages and challenges. I have to go out of my way to build on my undergraduate teaching experience. But, once identified, these issues are overcome by connecting with people at the nearby University of Oxford, and with my wider professional network.

For me the chance to work abroad is a big draw for a scientific career; it built my confidence and expanded my professional network as well as providing a great experience. Coming back to the UK was right for me at the time but I’d not rule out going abroad again.


© The Physiological Society

‘Establishing a life outside of work has been vital in putting my work here into perspective, and makes those inevitable scientific frustrations far easier to deal with.’ – Chris Shannon, University of Texas Health Science Centre, USA

The quest for the Holy Grail of lectureship
by Gisela Helfer, Lecturer, University of Bradford, UK

After I graduated in Zoology at the University of Salzburg, Austria, I worked at the Max Planck Institute for Ornithology in Andechs, Germany. Here I found my love for science in general and chronobiology in particular. From Andechs, I started my northwards journey, first to do a PhD at the University of Birmingham and then to postdoc at the Rowett Institute in Aberdeen. Throughout my journey, I was very fortunate to meet some amazing scientists, mentors as well as peers, and it was always my ambition to succeed in academia. Six years of postdocing, three moves and two children later, I finally found the Holy Grail in beautiful Yorkshire. In March 2016, I started my permanent lectureship at the University of Bradford.

Academia has one of the longest apprenticeships that I am aware of. Undergraduate studies, plus/minus masters studies, PhD studies and then several years of postdocing. For me, this totalled to 14 years of apprenticeship. Despite this long training, I was little prepared for the job of a lecturer. Yes, I had some teaching experience. I supervised students in the lab, I occasionally lectured to undergrads and I even worked a few months as a teaching fellow. In my CV I called this ‘extensive teaching experience’ – little did I know. Because in reality I spent all my days and often nights (the joys of circadian rhythms research) in the lab or in the animal house. And I loved every minute of it!


© Wellcome Library, London.

Now, I am rarely in the #Helferlab. The brand-new set of pipettes that I proudly bought from my first grant is now exclusively used by my students, while I spend my time rushing from place to place. I run to see undergrads or I run to one of my countless meetings.

I admit that I miss being a postdoc. I miss being in the lab from morning to evening, I miss having a supervisor who keeps me right (although my mentor at the Rowett is only a phone call away) and I miss the untroubled life of only being responsible for the next set of experiments. Of course, I do not miss the dreadful months before the contract comes to an end.

Despite all of this, I enjoy being a lecturer. While the holy grail is not as shiny and golden as I thought it would be, the journey was certainly worth it, and I would do it all over again. Next goal: professorship.

This article was compiled by Jo Edward Lewis. You can read more testimonies in the original article in our magazine, Physiology News.

Open education: a creative approach to learning and teaching

By Vivien Rolfe, Associate Head of Department, UWE Bristol, UK, @vivienrolfe

A longer version of this article originally appeared in our magazine, Physiology News.

Open education, a means of widening access to education and materials, is not a new idea. Universities and teaching institutions have been inviting the public through their doors for centuries, and in more recent times ‘open’ universities have further championed the widening of access to formal education.

Open education was a dominant philosophy and practice in the 1970s. Unstructured curricula fostered creativity and supported diversity in learning, and knowledge was shared beyond the institution. The present reiteration of open education has similar underpinning ideals: providing an education system that shares, and is more inclusive and equitable.


Open education – from content to practice

The relationship between shared open educational resources (OERs) and emerging open education practices is a hot topic of debate. Great work within schools, colleges and universities has clearly emerged through either the generation of openly licensed content (a good starting point), or the development of open practice and pedagogy.

A widely accepted framework for practice development is David Wiley’s ‘5 R’s’ (Wiley, 2014).  They stand for Retain (you control what happens to the resources you share) through to Reuse, Revise, Remix and Redistribute. This, in my experience, is a useful concept for teachers who aspire to develop their open practice

Open practice can extend the utility of our academic work within our institution, and even beyond the walls of our universities to a wider community of learners. In the UK, some notable examples include the University of Lincoln ‘Student as Producer’ project where students engaged as co-creators of open content, and the open photography course #Phonar at the University of Coventry which invited public collaboration and led to students working with professional communities as part of their learning.


Much of the UK activity stemmed from the 2009 – 2012 HEFCE-funded Open Educational Resource programme. Over 85 projects spanned most subject disciplines, and were seminal in building the community of open practitioners that thrives today by bringing them together in an annual conference organised by the Association of Learning Technology (#OERXX). I have reported the reach and impact of the OERs produced by these projects, and of using web marketing techniques to share content online (Rolfe, 2016).

Open practice for life science practicals

My recent work has explored open pedagogies in an attempt to address challenges facing laboratory practical teaching. Practicals are timetabled laboratory events, and it is well documented that teaching staff and technical teams struggle to address the gaps between school and university in terms of laboratory experience, for an ever-increasing number of students (Coward and Gray, 2014). Student criticisms include no buzz, repetitive nature and lack of social engagement (Wilson, Adams and Arkle, 2008).


So in my experience, what are some of the benefits and challenges of open educational practises in practicals?

Open education projects at De Montfort University included OERs on laboratory skills. Still accessible today via the project website and YouTube, these relatively low quality materials by today’s standards, were popular with students and boosted their confidence before entering the laboratory for the first time: “[Virtual Analytical Laboratory] has been very useful in easing my nerves before lab sessions” (Biomedical Science student, Rolfe, 2009). These resources were then embedded within the timetable with students working through workbooks prior to entering the lab. Soon, students were creating video of their own laboratory work and sharing these either informally with each other through social media, or as part of the project website. The laboratory technical teams also created resources in areas they thought students particularly struggled with. One of the benefits cited by staff was they needed to spend less time repeating basic instructions as students had an overview of the fundamental skills.

Other applications of open education included students accessing resources by QR codes at different workstations to introduce them to different techniques, which helped to cater for large student numbers in the lab in a more effective way. Students were also engaged in producing multiple-choice assessment questions, later shared as OERs accompanying resources on the project website.


Longer term, open education led to changes to the learning culture itself, with students taking control and implementing their own ideas, such as photographing histology images using iPhones for sharing as OER on the Google service Picasa, and later a Facebook discussion group. Some of the lasting impact of this work is the cross-university interest it generated – for example technology and arts students becoming interested in science projects, and the OER being available globally to support informal and formal learning, providing new insights and perspectives for students (Rolfe, 2016).

As more evidence is gathered as to the benefits and uses of OER and open practices, a new theoretical basis for open practical pedagogies may emerge. What is important is that we continue to openly share our case studies of teaching practice to build a fuller picture. That way, larger communities of teachers can grow and benefit:

“It has changed my practice in terms of whenever I’m doing anything I think how could this be an OER or how could it supplement what I’m doing”. (Microbiology lecturer).

Read the full-length version of this article in our magazine, Physiology News.


Coward, K., and Gray, J. V., 2014. Audit of Practical Work Undertaken Accessed 12 May 2017].

Rolfe, V., 2009. Development of a Virtual Analytical Laboratory (VAL) multimedia resource to support student transition to laboratory science at university. HEA Bioscience Case Study. pp. 1-5.

Rolfe, V., 2016.  Web Strategies for the Curation and Discovery of Open Educational Resources. Open Praxis, 8(4). [Accessed 12 May 2017].

Wiley, D., 2014. The Access Compromise and the 5th R. [online] [Accessed 12 May 2017].

Wilson, J., Adams, D. J. and Arkle, S., 2008. 1st Year Practicals–their role in developing future Bioscientists. Leeds, the Higher education Academy Centre for Bioscience. [online] [Accessed 12 May 2017].

Stress and the gut – it’s not all in your mind (Part 2)

By Kim E. Barrett, Division of Gastroenterology, Department of Medicine, University of California, San Diego, USA, @Jphysiol_eic.

This article originally appeared in our magazine, Physiology News.

The numerous microbes living inside of us help break down nutrients and “educate” our immune system to fight infection, but how do they help us respond to stress?

The microbiota as a mediator of responses to stress

Gut microbes change when people have intestinal diseases, such as inflammatory bowel diseases and irritable bowel syndrome. Indeed, some of the characteristics of these diseases can be transferred to animals in the lab that lack microbes, using microbes from diseased mice or humans. It is also becoming increasingly clear that gut microbes and their products may have effects well beyond the confines of the intestine itself.

Perhaps the most intriguing aspects of this area of research is that which ties the composition of the gut microbiome to brain function and the brain’s response to stress. Further, the adverse effects of stressful situations on gut function depend on the presence of intestinal microbes. To date, research supports bi-directional communication between the gut and brain (pictured below) that influences the normal function of both bowel and brain alike. This may explain, for example, why some digestive and psychiatric disorders go hand-in-hand (Gareau, 2016).

gut brain

Bi-directional communication between the gut and brain.

Evidence in human patients largely shows correlation not causation so far. Still, it is intriguing to observe that derangements in the microbiome have been associated with many conditions, including depression, autism, schizophrenia and perhaps even Parkinson’s disease (Dinan & Cryan, 2017).

Therapeutic manipulation of the microbiota – from probiotics to transplants

So if both intestinal and neuropsychiatric conditions are potentially caused by changes in the gut microbes (at least in part), and if such alterations also mediate the impact of stress on the relevant organ systems, can we mitigate these outcomes by targeting the microbiota?

Several approaches have been posited to have either positive or negative effects on the make-up of the gut microbiota and its intestinal and extra-intestinal influences.  Perhaps the most obvious of these is the diet. While the gut microbiota was at one time felt to be relatively immutable in adulthood, improved  techniques indicate that its make-up, in fact, is profoundly influenced by the composition of the diet and even by the timing of meals. For example, Western diets, high in meat and fat, decrease the diversity of the microbiota (and may even promote the emergence of pathogenic properties in commensals), whereas diets rich in plant-based fibre increase it.


Another approach to targeting the microbiota is the use of antibiotics, although for the reasons discussed in Part 1, these are likely to be mainly deleterious, particularly early in life. The composition of the microbiota can also be altered directly by the administration of probiotics, which are commensal microorganisms (the host benefits, while the microbes are unaffected) selected for their apparent health benefits that can be taken orally.  Studies in animal models demonstrate that probiotics can improve both gut and cognitive function in animals exposed to a variety of stressors, or can negate the cognitive dysfunction accompanying intestinal inflammation or infection.  However, not all probiotics are created equal, and much work remains to be done both to validate animal studies in human clinical trials, and to define characteristics of probiotic strains that predict efficacy in a given clinical setting.

Perhaps the approach to targeting the microbiota that has attracted the most recent public attention is the practice known as faecal microbial transplant (FMT), where faecal material is transferred from a healthy donor (often a relative) to someone suffering from a specific intestinal or extraintestinal disease.  Enthusiasm for FMT derived initially from its dramatic efficacy in some patients suffering from disabling and persistent diarrheal disease as well as other symptoms associated with treatment-resistant infections by C. diff (a harmful bacteria).  More recently, there have been encouraging data suggesting that FMT may be effective in producing remission in inflammatory bowel disease, although the long-term consequences are unknown, and larger, well-controlled studies are needed.  Exploratory reports even suggest beneficial effects of FMT on gastrointestinal and behavioural symptoms of autism, or in obesity and metabolic syndrome (a cluster of conditions that occur together and increase your risk of heart disease, stroke and other conditions), but much further work is needed to validate these preliminary data.  Ideally, FMT procedures should be conducted under carefully-controlled and physician-supervised conditions to screen for the potential presence of pathogens or toxins.  Nevertheless, despite the obvious “yuck” factor, “do-it-yourself” instructions can readily be found online (there are even Facebook groups), and some individuals are sufficiently distressed by their condition to give it a try.


Yep, this is exactly what you think it is.

Mitigating negative effects of stress

In conclusion, it is clear that our response to stress, whether manifested in our thought patterns or in our gut, is dramatically shaped by the microbiota that resides in the intestines.  Particularly in humans, studies conducted to date have largely been confined to cataloguing the key players in a given setting, but animal data are provocative, and studies focusing on microbes’ roles and functions in humans will doubtless follow.   No matter what, in the coming years, the explosive growth of studies aiming to target the microbiota for health benefits should give us a much better understanding of which approach, if any, is likely to be most beneficial for a given condition and even a given individual, since host factors clearly can also impact our microbial composition.  This work holds the promise of ameliorating negative effects of stress, and perhaps may offer new avenues for the therapy or even prevention of the myriad of stress-related disease states that are increasing in incidence in developed countries.


Dinan TG & Cryan JF. (2017). Gut instincts: microbiota as a key regulator of brain development, ageing and neurodegeneration. The Journal of physiology 595, 489-503.

Gareau MG. (2016). Cognitive function and the microbiome. International Review of Neurobiology 131, 227-246.


Stress and the gut – it’s not all in your mind (Part 1)

By Kim E. Barrett, Division of Gastroenterology, Department of Medicine, University of California, San Diego, USA, @Jphysiol_eic.

This article originally appeared in our magazine, Physiology News.

We all know that stress has an impact on the function of our digestive system. Whether it is the transient butterflies that accompany an exam or an interview, or the more toxic consequences of chronic stress, our experience of our world and its challenges can profoundly alter our digestion, absorption of nutrients, and excretion.

What has been less fully appreciated, until recently, is that communication between the brain and gut is bi-directional. Gut illnesses may be accompanied by brain disorders, such as anxiety, depression, and memory problems.  The brain and spinal cord are in constant communication with the gut, in part via the “little brain” – the nerves present in the gut that communicate with the brain.

While we humans like to think that we are masters of our own universe, in fact we, along with all other beings, are superorganisms. Our bodies consist not only of our own cells and genome, but also of distinctive populations of ‘friendly microbes’, along with their genes and ability to break down compounds. This so-called “microbiome” is made up mostly of bacteria, the best-studied populations, but also other microbes such as fungi and viruses (which are only now beginning to be examined).  Specialized groups of microbes inhabit various parts of our body, such as the intestines, mouth, skin, lungs, and genitals. The most extensively characterized of these microbiomes is the collection of bacteria in the gut, consisting of thousands of species in a typical healthy human adult. They reside throughout the intestines, but are most heavily concentrated in the colon. There are as many as 1014 of them throughout the gut. That’s ten times the number of human cells in the entire body (Sekirov et al., 2010). Recently, the 10:1 ratio has been disputed, with a claim that the numbers of human cells and gut bacteria are of the same order of magnitude (Sender et al., 2016). Even if this true, the microbes collectively have more genes than our cells do.

We are rapidly learning the ways in which these gut microbes may be important mediators of the cross-talk between the gut and brain. They are, in turn, influenced by environmental conditions, such as stress and diet, in ways that change their impact on both our thinking and digestion.

gut brain


Friendly microbes – what do they do for us?

Microbes, in the gut or elsewhere, are not essential for life, as illustrated by the ability to raise animals in a sterile environment in the lab. Nevertheless, the gut microbes in particular offer several advantages to the organism they inhabit. For us, they break down nutrients we can’t, such as dietary fibre, drugs, carcinogens, and compounds that break down into vitamins.  Similarly, the microbiota “educate” the immune system of organs such as our lungs and intestines to fight foreign substances but tolerate the proteins of broken-down food or other harmless microbes.

The organisms of the microbiome also defend against pathogens by crowding them out, producing substances that kill bacteria or keep them from reproducing, or causing the host to create those lethal compounds itself. For this reason, antibiotics that kill beneficial microbes can render patients susceptible to intestinal infections and overgrowth of harmful bacteria, such as Clostridium difficile (C. diff).

gut brain 2

3D cellular model of an intestine by Ben Mellows, PhD Student, University of Reading, UK

Gut microbes and birth

We think that gut microbes exist in the body immediately after birth, although some controversial data suggests the presence of microbes in the fetus before birth. Animals without microbes can be born via Caesarean section (C-section), implying that even if there are microbes in the womb, organisms don’t need them to survive (Perez-Munoz et al., 2017).

For babies delivered vaginally, their gut microbes are initially very similar to the mother’s vaginal microbiota, whereas they differ substantially for babies delivered by C-section. An intriguing recent study partially restored “normal” microbes in the gut, mouth, and skin by exposing babies delivered via C-section to the mother’s vaginal fluids. The authors thought that this might reverse the known association between C-section deliveries and an increased risk for immune and metabolic disorders (Dominguez-Bello et al., 2016).

For the first year or two of life, the baby’s microbes are relatively simple and variable, but they gradually take on the characteristics of a mature, adult-like microbiome. These early years are also a critical period for maturation of the immune system, so it makes sense that disrupting the maturation of the infant’s microbes also predisposes them to autoimmune and allergic diseases. For example, the increasing tendency to protect babies from germs or an excessive early-life use of antibiotics may set them up for an increased later risk of asthma, metabolic disease or obesity. This is called the “hygiene hypothesis” (Schulfer & Blaser, 2015).

Stay tuned for the part 2 of the series next week to learn about how gut microbes respond to stress, and the efficacy of therapeutics, from probiotics to transplants.


Dominguez-Bello MG, De Jesus-Laboy KM, Shen N, Cox LM, Amir A, Gonzalez A, Bokulich NA, Song SJ, Hoashi M, Rivera-Vinas JI, Mendez K, Knight R & Clemente JC. (2016). Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. Nat Med 22, 250-253.

Perez-Munoz ME, Arrieta MC, Ramer-Tait AE & Walter J. (2017). A critical assessment of the “sterile womb” and “in utero colonization” hypotheses: implications for research on the pioneer infant microbiome. Microbiome 5, 48.

Schulfer A & Blaser MJ. (2015). Risks of antibiotic exposures early in life on the developing microbiome. PLoS Pathog 11, e1004903.

Sekirov I, Russell SL, Antunes LC & Finlay BB. (2010). Gut microbiota in health and disease. Physiological reviews 90, 859-904.