Your Gut health Consumer Information Forum - Your questions answered

True or false: the vegan diet is the most cancer-preventing and best cancer-fighting diet?

False. Eliminating animal products from the diet does not necessarily mean the diet is automatically healthier. You could be a vegan consuming a diet high in refined carbohydrates and your overall diet could be of low nutritional value. Diets high in fruits, vegetables & wholegrains are an important part of preventing cancer, because they provide fibre which is beneficial for the gut biome as well as antioxidants and phytochemicals that help protect cells. Including non-animal sources of protein in your diet such as beans, lentil and nuts is a good idea and limiting processed and fatty animal products is also a good idea.


What about patients with history of eating disorders? Does a focus on diet increase stress and therefore, reduce benefits?

Patients with eating disorders should work with their health professional to set goals that are specific to them. Depending on the severity of the eating disorder it may not be appropriate to place any focus on eating for the gut biome.  The focus would need to be normalising eating patterns and stabilising weight and attitudes to foods.


I have CLL infiltrating in liver causes pain liver elevated 3 enzymes; which is considered rare. What diet would be helpful to manage or improve my liver health.

Most of the research on gut health and disease is in very early stages. There is nothing that I have come across that is specific to CLL or liver health and the gut biome. In terms of what diet is best for your liver problems, you should speak to your medical team and assess if a referral to a dietitian could be beneficial. Its best to address these questions knowing all the medical information.


Can a person survive eating only medically formulated liquid such as Ensure, Sustagen, Resource?

Yes, some nutrition supplements are nutritionally complete and many people do survive with this being there only form on nutrition. It would be interesting to study the changes to the gut biome, but this has not been investigated yet. Definitely more research is needed.


Are you researching conditions such as chronic idiopathic nausea? What is the best diet for a patient with chronic nausea? What causes it?

No, I am unaware of any link or research that considers gut biome and chronic idiopathic nausea.


What effect does a glass of wine with a meal have on the gut and microbiome?

Alcohol in general has a negative impact on the gut biome, but red wine in moderation appear to be an exception. Red wine contains polyphenols which are phytochemicals that help protect cells and interestingly they also appear to improve beneficial bacteria and decrease harmful bacteria.


What is the effect on the microbiome of having a colonic performed, or completing a salt water cleanse?

I’m not sure that colonic cleanse have been widely studies. It would appear from case reports, that the profile of bacteria decreases temporarily and then returns to normal. Colonic cleans are considered an alternative therapy and not generally recommended.


Can Dysbiosis have an effect on hypertension? Are there sympathetic hot-spots along the gut and how might this effect contribute to the disease?


Gut microbiome and hypertension is a really interesting area of research. People with hypertension have a distinct microbiome differences compared to people who do not have hypertension. Mechanisms for this are being investigated and, it appears that the bacteria are able to communicate with the sympathetic nervous system and influence blood pressure. Short chain fatty acids that are produced by bacteria will communicate in ways that can raise or lower blood pressure. It is uncertain what role genetics plays in this and if some people are more likely to respond to changes in gut biome than others.



Does IBS increase your chance of bowel cancer?

The available evidence does not support that people with irritable bowel have an increased risk of bowel cancers.



Are there any studies or findings related to the effect of exercise on the gut microbiome

There are both animal and human studies that investigate the impact of exercise and gut microbiome. Just like many of the diet related studies, they are in early stages and more research is needed to better understand the link with disease. It does appear that exercise improves the profile of bacteria and enhances the ratio of bacteria that produce short chain fatty acid.


Does the state of fibre consumed affect its performance in the gut for example frozen veggies, frozen fruits.


I am not aware of any specific research on this, but I would think that freezing vegetables would not change the fibre. Any benefit that fibre provides is likely to be retained by that food. Theoretically fresh fruits and vegetables may contain other bacteria that may or may not be beneficial to the gut biome and this could potentially be lost in frozen foods.


What are the effects of and differences between a standard western/omnivorous diet compared to a plant-based diet on the gut microbiome?


It is difficult to make general statements promoting one type of diet over another. The quality of a person’s diet and the impact on the gut biome is not specifically linked to the intake of plant based foods v’s having a meat intake. Western diets are known for having a higher intake of processed foods, too much fat, salt and refined sugars. Because of these factors and the generally low intake of fruits, vegetables and wholegrains, the gut biome is less diverse and has less of the bacteria that we recognise as being beneficial.  

What would the ideal daily diet look like to optimise gut health?

Fibre is the key component of the gut biome, the bacteria rely on fibre as a fuel source. Studies have shown that consuming 25-30g of fibre improves the bacteria that produce short chain fatty acids which in turn have health benefits for us. The fibre should come from a variety of source including fruits, vegetable, whole grains and legumes. We are also understanding that recommendations we have always made such as lower sugar, lower salt and deceasing saturated fats also have an influence on the gut biome and the mechanism are becoming better understood.

 What is the effect of intermittent fasting or just fasting on the gut?

Animal studies on fasting have been very interesting and demonstrated an improvement in survival as well as protection from some diseases. Early research suggests that fasting could allow the gut to rest and improve the health of the intestines. The bacteria also appear to benefit from periods of fasting and there are changes that occur that result in an improved profile of bacteria. We do not have enough studies to tell us the best way to fast or large enough studies to detect differences in different people.

Probiotics and prebiotics

·         For how long is it ok to take probiotics

Minimal evidence to show long term benefit of taking probiotics. Evidence suggests that diversity is the key – so taking one type of probiotic long term may not be as beneficial as taking several different strains.  Probiotics are considered safe overall for healthy people but risks may be greater in immunocompromised people.

·         Is that mean we should be taking tablets to get probiotics more efficient than whole food??

Eating a diet high in whole foods will support bacteria growth. Taking probiotics in a tablet form – so long as they survive the trip through the stomach acids- may be more efficient than taking probiotics in a liquid form.

·         Do you need to take probiotics at the same time everyday?

There is no evidence to suggest that probiotics should be taken at the same time everyday. There is some evidence to suggest that taking probiotics with prebiotics or after food high in fibre is more effective at supporting bacterial growth.

·         Do non-dairy yoghurts contain probiotics?

They can. Check the product label for a listing of probiotic strains

·         Are probiotics useful for cancer related constipation?

Constipation, especially cancer related, is a multifactorial condition. It is unlikely that one intervention such as taking probiotics will alleviate the problem. A diet high in fiber, which in itself supports a beneficial microbiome, is likely to be more effective.

·         Are probiotics safe for me to take if my white call count is low?

There are some risks associated with taking probiotics, especially in people who are immunosuppressed, including bacterial translocation across the gut into the blood stream. It is not recommended that highly immunosuppressed people take probiotics for that reason.

·         Can you take probiotics during antibiotics or should you wait until after your course of antibiotics?

There is evidence to suggest that taking probiotics at the same time as antibiotics is beneficial and has in fact been recommended in France for decades.


·         Dr. Monica, why isnt the FMT done via colonoscopy instead of via mouth (gastroendoscopy) ?

The procedure can been done via either route, however in order to deliver the FMT to the site it will be most beneficial (large intestine), the endoscopic route is better. Also there is a significant risk of regurgitation or aspiration with the gastro route of administration.

 Infections and disease other

·         Can a thing like Bali belly clear out your gut biome? And if so how do you replenish?

There is some evidence to suggest that things like food poisoning can disrupt your microbiome and change the relative abundance of different strains. These effects have been shown to persist for months after the episode of food poisoning and your microbiome may even be permanently altered.

·         What is the best way to regenerate and regulate the bowel after a ruptured appendix, sepsis infection, ileostomy bag and then ileostomy reversal 3 moths later?

Bowel regeneration is not possible, however good diet and lifestyle will support a healthy gut, which in turn will support a healthy biome

·         If I’ve been affected with aemoeba, am I infected forever?

No, if you are treated appropriately the amoeba will be completely cleared from your body.

Cancer tx outcome

·         Is there any research on how radiotherapy or chemotherapy alter the microbiome?

Research in this area is in its infancy and we hope to lead the field with world first longitudinal studies to examine changes over time with cancer therapies.

·         Is there such a thing as ‘leaky gut syndrome’? Most general doctors don’t acknowledge it.

The term leaky-gut syndrome describes a situation where there are microscopic gaps in the gut wall which allow bacteria to pass into the blood stream causing a low level systemic inflammation. Leaky gut is very hard to prove as you need to show both an increase in bacterial products in the blood as well as have a gut biopsy to show that there are microscopic gaps in the gut wall. For that reason most doctors are reluctant to diagnose someone with leaky gut syndrome. There is very little documented “proof” of it occurring.


·         Do topical antibiotics affect the gut microbiome?

Antibiotics applied topically are unlikely to reach the gut in high enough concentrations to affect the microbes in the gut directly. Taking antibiotics through the gastro-intestinal or intravenous route will.

·         Do the antibiotics that livestock are fed have an impact on our gut microbiome when we consume animal products?

No – the concentration of antibiotics in the meat we eat is too low to have any effect on our health.


·         What about the impact of stress on our microbiome and it’s expression?

Studies do show that stress affects the composition of the microbiome, as well as (at least in rats), the integrity of the gut lining. It should be noted that experiments usually demonstrate this with fairly severe stressors and it is unclear how well this translates to humans. In a recent study of American children who had been institutionalised (e.g. in orphanage) at a young age, their microbiome was shown to be different from children who had grown up in their family home, and this mapped on to activity in the brain in response to emotional stimuli. It is presumed that some of these changes are due to the effects of stress on the gut and brain. 

·         How much does stress change the gut?

Answered above

·         Have the patients in the SMILES trial been followed up long term?

No, not so far


·         Does the contraceptive pill effect biome.

Yes it does

·         Blocking testosterone in men changes the biome, does the contraceptive pill in blocking ovary testosterone production change the biome?

Yes modification of the microbiome have been described in women taking contraception with a possible link to inflammatory bowel disease in rare cases.



·         Would you considering doing an observational study looking at enterally fed patients and gut bacteria?

Yes why not, should be very interesting

·         Hi, I am curious about what role of bioinformatics plays in gut microbes research and how it will change the future understanding of gut.

We are able to DNA sequence the varying types of microbes colonising our gut. To manage this information Bioinformatics is needed as well as advanced computational biology. Both are used not just for the identification of microbes in the gut but to determine subgroups of microbes and how they may change over times, as well as correlate this data with clinical and biochemical data.

·         Are there any tests that assess microbiome composition and gut health?

We use metagenomics. Some facilities in QLD, like the Aussie Gut (Griffith University) and Microba, University of Queensland offer microbiome service. However, the data is very complex and can only be used effectively in the context of research with expert. At the University of Melbourne(PDI) and with the ACRF, metagenomic analysis service for research are available. There are several tests that we can do to assess the composition of the gut microbiome, the trick is to relate this to health outcomes. This requires longitudinal studies to assess changes in microbiome compostion and health over time. Yes totally agree with that and it needs supercomputing too.


·         How much do our genes affect the composition of our gut microbiome? How much is defined by our diet and how much by our genes?

The diet is very important and studies in Nature in the US in people from various ethnic background showed that diet, lifestyle and environment more than genetics is shaping the microbiome. But we are talking about healthy individuals. It is quite clear that it is not the case with sick people or people with a genetic modification affecting immune balance in the gut for instance.

Demystifying casemix funding and hospital-acquired complication penalties: the coding continuum

Jake Valentine.jpg

Mr Jake Valentine

Jake has an interest in enhancing the utility of hospital discharge coding data for infectious disease surveillance in patients with cancer. Jake works closely with relevant stakeholders to ensure that Australia's capitation Activity Based Funding model is sustainable and equitable for all Australian hospitals managing healthcare-associated infections in hospitalised cancer patients.

In Australia, Weighted Inlier Equivalent Separation (WIES) funding works in a capitation Activity Based Funding (ABF) system, meaning that hospitals are funded on the basis of their patient case-mix. In Victoria, hospitals are grouped into local hospital networks (LHN) based on their geographical proximity to each other. Rather than be funded at an individual hospital-level, Victorian healthcare facilities are funded as LHNs. This means that one LHN will receive the same level of funding in WIES as compared to a neighbouring LHN which may receive more or less funding in WIES depending on the complexity of their patient case-mix. The principles underpinning ABF ensure there is equitable access to Commonwealth funding across all LHNs and Australian jurisdictions; is technical efficiency and sustainability in reducing long-term health expenditures; and most importantly, is patient, not provider focussed.  

 The Commonwealth Government reimburses states and territories approximately 45% of healthcare expenditure, with the remaining paid for by the respective jurisdiction. The amount paid for by the Commonwealth Government is called the National Efficient Price (NEP) (or WIES base rate in Victoria). The NEP typically increases each financial year to reflect the rising cost of healthcare. For example, the WIES base rate in 2016/17 was $4,640, meaning the Federal Government will pay a fixed rate of $4,640 for each episode-of-care, or separation. However, this can change depending on the type of Australian Refined Diagnosis Related Group (AR-DRG) allocated to this episode-of-care. Each AR-DRG carries its own inlier weight. If the inlier weight > 1.0, the Commonwealth will pay more than the NEP. Conversely, if the AR-DRG < 1.0, the LHN will receive less than the NEP in that given financial year. Using the same principle, if the inlier weight = 1.0, the LHN will receive $4,640 for that episode-of-care. To complicate things further, the amount of WIES funding varies depending on the patient’s LOS. Let’s discuss this together by referring to my WIES funding algorithm (Figure 1):

fig 1.jpg

Figure 1. WIES funding algorithm. AR-DRG, Australian Refined Diagnosis Related Group; FY, financial year; HAI, healthcare-associated infection; ICD-10-AM, International Statistical Classification of Diseases and Related Health Problems, Tenth Revision, Australian Modification; ICU, intensive care unit; IHPA, Independent Hospital Pricing Authority; LOS, length of stay; NEP, National Efficient Price; NHCDC, National Hospital Cost Data Collection; WIES, Weighted Inlier Equivalent Separation

The technical specifications of WIES funding are complex, but are central in understanding the importance of robust and reproducible administrative coding data for health services provision. The State Government of Victoria’s Department of Health and Human Services’ current funding model for acute inpatient services is called WIES (also known as the National Weighted Activity Units (NWAU) in other states and territories). There are four key steps in determining the level of WIES funding provided from Commonwealth and State Governments (Figure 1):

1.      Step 1) Determine the AR-DRG

2.      Step 2) WIES weight plus adjustment

3.      Step 3) Determine inlier equivalent

4.      Step 4) Calculate WIES payment

Step 1) Inpatient diagnoses will be recorded in a medical chart. This information is then codified into ICD-10-AM codes, and will typically fall under one of three categories – (i) primary diagnoses, (ii) secondary diagnoses, and (iii) complications (e.g. healthcare-associated infections (HAI)). These codes, along with the patient’s age, gender, LOS (in days), procedures and other clinical characteristics are then further coded into a single AR-DRG code. 

Step 2) Length of stay (LOS) data for each AR-DRG is submitted to the Independent Hospital Pricing Authority (IHPA) from every public and private hospital in Australia. The IHPA then standardise or ‘average out’ the LOS for each AR-DRG in the National Hospital Cost Data Collection (NHCDC), giving us a low and high inlier boundary. For example, AR-DRG A01Z (2016/17 FY) has a LOS inlier boundary of 10 – 93 days (average: 27.9 days). This means most (but not all) patients designated code A01Z have a LOS between 10 – 93 days. In this instance, the inlier weight for that given AR-DRG is multiplied by the NEP to determine the level of WIES funding. Simple enough, right? But what happens if the patient’s LOS doesn’t fall in the inlier boundary?

Step 3) If the patient’s LOS falls below the low inlier boundary for that given AR-DRG, then a low outlier per diem weight is applied. Similarly, if it falls above the upper boundary, then a high outlier per diem weight is applied. This information is freely available in the NHCDC.

Step 4) Now for the business end of WIES funding: calculating payments. Depending on the patient’s LOS, one of four scenarios typically occur. The best illustration of this is provided in Figure 1. In addition, some patients are more expensive than others irrespective of their AR-DRG, for example, if a patient is admitted to the ICU and/or requires mechanical ventilation. In this instance, an additional co-payment in WIES is provided to LHNs to reflect the heightened cost in managing these patients.  

fig 2.png

Figure 2. How Activity Based Funding is back-paid to acute public hospitals depending on patient length of stay (in days). Schematic adapted from the Independent Hospital Pricing Authority National Pricing Model Technical Specifications 2012-2013.

For healthcare providers, there is a period during inpatient stay where LHNs could receive more funding than what they pay in healthcare costs as per the WIES algorithm. Arbitrarily depicted in Figure 2, the red line is WIES payment and the green line is how much the hospital is spending in healthcare costs. Where the red line is situated above the green reflects the cost accrued is less than the funding paid by governments (i.e. a profitable period for hospitals!). When we enter the inlier boundary period for that AR-DRG, WIES funding is fixed, despite the fact that the hospital will be spending more and more each day in healthcare costs. Where we go above and beyond the high inlier boundary, WIES funding will increase on a per diem basis, but may not reflect the amount the hospital is spending in managing these complex patients.

Let’s bring this full circle for infections in cancer. The Federal Government will now withhold a percentage of WIES payments to LHNs when ICD-10-AM codes denoting certain HAIs are reported to the IHPA. This is called the Hospital-Acquired Complication policy. Historically, ICD-10-AM codes miss true HAI diagnoses in the medical chart, or in some instances, code an infection even when one was never present! In cancer patients, their immune system is suppressed, placing them at heightened risk of infection as compared to a non-cancer patient case-mix. This means more infections are occurring in cancer patients, increasing the probability of miscoding patients as having a HAI. Returning to Step 1 of the WIES funding algorithm, this is bad news, because cancer hospitals may be unfairly penalised in WIES funding if these codes are reported to the IHPA (despite these HAIs never occurring in the first place). The consequence – a negative funding adjustment is applied to this episode-of-care where a HAI code is reported, meaning the LHN will receive a percentage (and not the full amount) of funding in WIES, leaving the LHN to find alternative funding to fund the difference. Added to this is the fact that cancer patients with HAIs have an increased LOS, meaning these patients are likely to extend beyond the high inlier LOS boundary where WIES funding received may not reflect hospital expenditure in managing these HAIs.

The objective of the HAC policy is to provide a funding disincentive to encourage healthcare facilities to prevent the occurrence of HACs, thus improving patient safety and the quality of inpatient care. The issue … HAC penalties are contingent on the quality of administrative coding data, with some LHNs performing better than others in coding true cases of HAIs. Coding data have a broader worldwide reach, enabling system-wide health services research and monitoring of performance markers in cancer patients. Administrative HAC coding, as it stands, is not optimised for cancer patients. Efforts are needed to ensure that ICD-10-AM codes denoting HAIs, particularly in high-risk cancer patients, are robust and reproducible enough to accurately measure quality improvement programmes.  

More resources :

 1.      Valentine JC, Haeusler GM, Worth LJ, Thursky KA. Sepsis incidence and mortality are underestimated in Australian intensive care unit administrative data. Med J Aust 2019; 210(4): 188-.e1.

2.      Calderwood et al., Centers for medicare and medicaid services hospital-acquired conditions policy for central line-associated bloodstream infection (CLABSI) and cather-associated urinary tract infection (CAUTI) shows minimal impact on hospital reimbursement. Infect Control Hosp Epidemiol 2018; 39(8):897-901

3.      Lee et al., Effect of Nonpayment for Preventable Infections in U.S. Hospitals. N Engl J Med 2012; 367(15):1428-1437

4.      Rhee et al., Impact of the 2012 medicaid health care-acquired conditions policy on catheter-associated urinary tract infection and vascular catheter-associated infection billing. Open Forum Infect Dis 2018; 5(9):1-4

5.      Pricing and funding for safety and quality. Sydney, New South Wales, Australia: Independent Hospital Pricing Authority, 2018-19:1-52.

6.      Kawai AT, Calderwood MS, Jin R, et al. Impact of the Centers for Medicare and Medicaid Services Hospital-Acquired Conditions Policy on Billing Rates for 2 Targeted Healthcare-Associated Infections. Infect Control Hosp Epidemiol 2015; 36(8): 871-7.

7.      Risk adjustment model for Hospital Acquired Complications - Technical Specifications. Sydney, New South Wales, Australia: Independent Hospital Pricing Authority, 2017:64.

8.      Shepheard J, Lapiz E, Read C, Jackson TJ. Reconciling hospital-acquired complications and CHADx+ in Victorian coded hospital data. Health Inf Manag 2018: 1-11.