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Supplemental material, sj-docx-1-cpa-10.1177_07067437221150508 for Feasibility, Acceptability, and Safety of Faecal Microbiota Transplantation in the Treatment of Major Depressive Disorder: A Pilot Randomized Controlled Trial by Jessica Emily Green, Michael Berk, Mohammadreza Mohebbi, Amy Loughman, Amelia J. McGuinness, David Castle, Mary Lou Chatterton, Joahna Perez, Philip Strandwitz, Eugene Athan, Christopher Hair, Andrew A. Nierenberg, John F. Cryan and Felice Jacka in The Canadian Journal of Psychiatry

See submitted Gut Feelings manuscript or ACTRN12617000795392 for trial background. The aim of the current analysis was to evaluate the effect of psychobiotics on the gut microbiome.

The role of the oral microbiome in mental health, and especially depressive and anxiety disorders, is poorly understood. This cross-sectional study aims to investigate the associations between the occurrence of specific bacterial species in the oral microbiome and the presence of depressive and anxiety symptoms in adults.

The microbiome-gut-brain-axis field is multidisciplinary, benefiting from the expertise of microbiology, ecology, psychiatry, computational biology, and epidemiology amongst other disciplines. As the field matures and moves beyond a basic demonstration of its relevance, it is critical that study design and analysis are robust and foster reproducibility. In this companion piece to Bugs as Features (Part 1), we present techniques from adjacent and disparate fields to enrich and inform the analysis of microbiome-gut-brain-axis data. Emerging techniques built specifically for the microbiome-gut-brain axis are also demonstrated. All of these methods are contextualised to inform several common challenges: how do we establish causality? How can we integrate data from multiple 'omics techniques? How might we account for the dynamicism of host-microbiome interactions? This perspective is offered to experienced and emerging microbiome scientists alike, to assist with these questions and others, at the study conception, design, analysis and interpretation stages of research., Comment: For main text: 20 pages, 2 figures; for supplementary analysis: 31 pages and 6 figures. Supplementary analysis generated using Rmarkdown by Thomaz F. S. Bastiaanssen. arXiv admin note: substantial text overlap with arXiv:2207.12475

The association between dairy products including milk, yogurt and cheese and markers of inflammation and oxidative stress is understudied in schoolchildren and warrants further population-based studies.

Research Questions Does diet and gut microbiota development interact during early childhood to influence preschool children’s behaviour?

Dairy products are generally considered part of a quality diet due to their rich nutritional profile and functional properties. The role of dairy products in diverse health outcomes such as cardiovascular disease, metabolic disease has also been extensively investigated. More recently, the human gut microbiota is being investigated as a key mediator between diet and health; however, there are few data to date on the gut microbiota composition correlates of dairy intake in humans. Therefore, we aim to conduct a population level cross-sectional analysis to assess the association between habitual dairy intake, including milk (non-fat, low-fat, whole fat), fermented dairy products (i.e. yogurt, cheese) and human gut microbiota composition. We will use data from a large, representative sample of men living in South-eastern Australia.

This document comprises the pre-registration of a study examining associations between gut microbiota composition between 12 to 24 months of age and cognitive development at 24 months.

Minor amendments

Despite advances in the treatment of anorexia nervosa (AN), current therapeutic approaches do not fully consider gastrointestinal (GI) disturbances. Nevertheless, addressing GI disturbances, both symptoms and disorders, is vital to improving treatment adherence and outcomes in people with AN. GI disturbances are complex and can be linked to a range of factors related to the eating disorder. Furthermore, aspects within treatment may contribute to the trajectory of GI disturbances and, in turn, AN symptomology. As nutritional rehabilitation is an imperative first step in the AN treatment, GI disturbances in people with AN pose a challenge for the dietitian and require careful consideration. Therefore, this survey aims to explore perceived knowledge, attitudes, and practices of dietitians treating AN and co-occurring GI disturbances. Results from this online survey will establish a foundational knowledge base for future research, clinician training needs, and the development of novel dietary therapies for people with AN and GI disturbances.

Poor muscle health has been associated with chronic inflammation. One of the proposed pathways is the gut microbiota, with an undesirable microbial composition potentially contributing to increased systemic inflammation. Conversely, butyrate-producing bacteria in the gut have been implicated in maintaining a healthy intestinal wall, by potentially reducing the permeability that has been theorised to contribute to systemic inflammation. Furthermore, increased presence of these butyrate-producing bacteria has been associated with good diet quality, as butyrate is a by-product of bacterial fermentation of fibre in the gut. Therefore, the current study aims to investigate the potential relationship/s between the gut microbiota, diet and muscle health, with a focus on the role of butyrate-producing bacteria as one of the proposed pathways.

This project is investigating the differences in gut bacteria, cognition and lifestyle factors (diet, physical activity and sleep) between healthy young, healthy older adults and individuals with Parkinson's disease.

Large-scale observational studies across diverse populations show ultra-processed foods (UPFs) contain lower levels of protein, fibre and essential vitamins and minerals (1-8) as well as higher levels of added sugar, saturated fat, sodium and overall energy compared to non-UPFs (2, 6-10). Given these nutrient profiles, UPFs are likely pro-inflammatory (11). This, however, has seldom been tested. Our recent systematic review and meta-analysis of observational studies found that to date only one cross-sectional study has assessed the association between consumption of UPFs and high-sensitivity C-reactive protein (hsCRP) (12). This study, conducted in the Brazilian population, concluded that while associations between UPFs and hsCRP were sex-specific and mediated by adiposity in women, elevated inflammation may be a possible underlying mechanism in the association between UPFs and chronic diseases (13). Considering that the pro-inflammatory potential of UPFs is not well characterised and given that systemic chronic inflammation is implicated in the aetiology of many chronic diseases (14), more research is needed. The Melbourne Collaborative Cohort Study (MCCS) is a project that aims to assess the links between diet and lifestyle and chronic non-communicable diseases, with European migrants included and deliberately recruited alongside Australian-born people to expand the span of diet and lifestyle exposures. The current study will build upon previous work by providing evidence in diverse and multicultural societies such as Australia where the average intake of UPFs may be higher than Brazil (6, 12) and where potential generalisability to other Anglo-European populations exists. The primary aim of this study is to utilise baseline data from the MCCS to undertake a cross-sectional analysis of the possible association between UPFs intake and inflammation (as measured by hsCRP) in Australian adults. Secondary aims include supplementary analyses that will test if part of the association between UPFs intake and hsCRP level is independent of anthropometrics and whether sex modifies this association.

Ultra-processed foods (UPFs), as characterised by the NOVA food classification system, are depleted of necessary dietary components such as the various fibres, polyphenols, omega-3 fatty acids and essential vitamins and minerals contained within whole vegetables, fruits, legumes, and grains, fatty fish, lean meats, nuts and seeds and other non-UPFs. Instead, the nutritional composition of UPFs commonly comprises elevated levels of calories, refined starches, sugar, sodium and saturated and trans-fats (1). These characteristic high caloric and nutrient poor UPF profiles are the foundation of “Western” and “proinflammatory” dietary patterns, both of which have been associated with the common mental disorder, depression (2, 3). Indeed, our recent systematic review and meta-analysis involving prospective observational studies and totalling more than 41,000 people initially free of depression showed that UPFs were associated with a 22% increased risk for future depression over a follow up period of between two to ten years (4). However, the link between UPFs and depression has not been tested in a more rigorous randomised, controlled trial (RCT) setting and ethical considerations mean that such trials are unlikely. As such, we seek to examine whether UPF intakes influence treatment response to dietary improvement in people with depressive illness. Using seven-day food diary data from the ‘Supporting the Modification of Lifestyle In Lowered Emotional States’ (SMILES, N=67) trial of people with moderate to severe major depressive disorder, the aims of this study are to: 1) undertake a cross-sectional analysis by pooling participants from both treatment conditions to assess the possible association between UPF intake and depressive symptomology at baseline 2) examine the potential effect modification of UPF intake at baseline as well as UPF intake change from baseline to follow-up on the relationship between treatment conditions and depressive symptomology at follow-up.

There has been a growing acknowledgement of the involvement of the gut microbiome - the collection of microbes that reside in our gut - in regulating our mood and behaviour. This phenomenon is referred to as the microbiome-gut-brain axis. While our techniques to measure the presence and abundance of these microbes have been steadily improving, the analysis of microbiome data is non-trivial. Here, we present a perspective on the concepts and foundations of data analysis and interpretation of microbiome experiments with a focus on the microbiome-gut-brain axis domain. We give an overview of foundational considerations prior to commencing analysis alongside the core microbiome analysis approaches of alpha diversity, beta diversity, differential feature abundance and functional inference. We emphasize the compositional data analysis (CoDA) paradigm. Further, this perspective features an extensive and heavily annotated microbiome analysis in R in the supplementary materials, as a resource for new and experienced bioinformaticians alike., For main text: 23 pages, 3 figures; for supplementary demonstration analysis: 31 pages and 12 figures. Supplementary demonstration analysis generated using Rmarkdown by Thomaz F. S. Bastiaanssen. Part I of a two-part piece

Currently, patient perspectives and experiences of gastrointestinal (GI) disturbances may not have been fully explored, yet are vital to furthering our understanding of the experience of an ED. Furthermore, exploring relationships between GI disturbances, ED symptoms and ED behaviours is essential to gain insights into the potential cumulative impact of these factors on treatment, and hence, inform the adaption of treatments accordingly. This project will elevate the voices of individuals with lived experience of ED in the research space investigating GI disturbances and their relationship to quality of life, as well as their broader role in the experience of the disorder, treatment and recovery.