Reviews

Over the past 20 years, members of the Cultech team have written a wide range of reviews discussing the gut microbiota and probiotics and adding to the understanding of the interplay between the gut, the microbiome and health and disease.

Williams CF, Walton GE, Jiang L, Plummer S, Garaiova I, Gibson GR. Comparative analysis of intestinal tract models. Annual Review of Food Science and Technology 2015; 6:329-50

The human gut is a complex ecosystem occupied by a diverse microbial community. Modulation of this microbiota impacts health and disease. The definitive way to investigate the impact of dietary intervention on the gut microbiota is a human trial. However, human trials are expensive and can be difficult to control; thus, initial screening is desirable. Utilization of a range of in vitro and in vivo models means that useful information can be gathered prior to the necessity for human intervention. This review discusses the benefits and limitations of these approaches.

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Corfe BM, Harden CJ, Bull M, Garaiova I. The multifactorial interplay of diet, the microbiome and appetite control: current knowledge and future challenges. Proceeding of the Nutrition Society 2015; 74(3): 235-44

The recent availability of high-throughput nucleic acid sequencing technologies has rapidly advanced approaches to analysing the role of the gut microbiome in governance of human health, including gut health, and also metabolic, cardiovascular and mental health, inter alia. Recent scientific studies suggest that energy intake (EI) perturbations at the population level cannot account for the current obesity epidemic, and significant work is investigating the potential role of the microbiome, and in particular its metabolic products, notably SCFA, predominantly acetate, propionate and butyrate, the last of which is an energy source for the epithelium of the large intestine. The energy yield from dietary residues may be a significant factor influencing energy balance. This review posits that the contribution towards EI is governed by EI diet composition (not just fibre), the composition of the microbiome and by the levels of physical activity. Furthermore, we hypothesise that these factors do not exist in a steady state, but rather are dynamic, with both short- and medium-term effects on appetite regulation. We suggest that the existing modelling strategies for bacterial dynamics, specifically for growth in chemostat culture, are of utility in understanding the dynamic interplay of diet, activity and microbiomic organisation. Such approaches may be informative in optimising the application of dietary and microbial therapy to promote health.

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Bull MJ, Plummer NT. Part 2: Treatments for Chronic Gastrointestinal Disease and Gut Dysbiosis. Integrative Medicine 2015; 14(1):25-33

Part 1 of this review discussed the connection between the human gut microbiota and health. Manipulation of the intestinal microbiota holds promise as a prospective therapy for gut dysbiosis, ameliorating symptoms of gastrointestinal and systemic diseases and restoring health. The concept of probiotics has existed for more than 100 y, and modern research methods have established sound scientific support for the perceived benefits of probiotic bacteria, which mainly include Lactobacillus and Bifidobacterium genera. On the basis of these evidence-based functional approaches, dietary interventions that supplement the normal diet with probiotics or prebiotics are now considered as potentially viable alternatives or adjuncts to the use of steroids, immunosuppressants, and/or surgical interventions. Studies investigating the impact on gastrointestinal disorders, such as diarrhoea, inflammatory bowel disease (IBD), irritable bowel syndrome (IBS); and systemic metabolic diseases, such as type 2 diabetes and obesity, in response to the use of probiotics and prebiotics are reviewed. Further, faecal microbial transplantation (FMT) is discussed as an exciting development in the treatment of gut dysbiosis using microbes.

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Integr Medicine 2014; 13(6):17-22

Part 1: The Human Gut Microbiome in Health and Disease.

Bull MJ1, Plummer NT1.

The bacterial cells harboured within the human gastrointestinal tract (GIT) outnumber the host’s cells by a factor of 10 and the genes encoded by the bacteria resident within the GIT outnumber their host’s genes by more than 100 times. These human digestive-tract associated microbes are referred to as the gut microbiome. The human gut microbiome and its role in both health and disease has been the subject of extensive research, establishing its involvement in human metabolism, nutrition, physiology, and immune function. Imbalance of the normal gut microbiota have been linked with gastrointestinal conditions such as inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS), and wider systemic manifestations of disease such as obesity, type 2 diabetes, and atopy. In the first part of this review, we evaluate our evolving knowledge of the development, complexity, and functionality of the healthy gut microbiota, and the ways in which the microbial community is perturbed in dysbiotic disease states; the second part of this review covers the role of interventions that have been shown to modulate and stabilize the gut microbiota and also to restore it to its healthy composition from the dysbiotic states seen in IBS, IBD, obesity, type 2 diabetes, and atopy.

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Bull M, Plummer S, Marchesi J, Mahenthiralingam E. The life history of Lactobacillus acidophilus as a probiotic: a tale of revisionary taxonomy, misidentification and commercial success. FEMS Microbiology Letters 2013;doi 10.1111/1574-6968.12293

Lactobacillus acidophilus is a commercially significant bacterial probiotic, originally isolated from the human gastrointestinal tract and designated Bacillus acidophilus in 1900. Throughout the development of methods to identify and characterise bacteria, L. acidophilus has undergone multiple taxonomic revisions and is now the type species of a phylogenetic subgroup in the highly diverse and heterogeneous Lactobacillus genus. As a result of the limitations of differentiating phenotypically similar species by morphological and biochemical means and revisionary nature of Lactobacillus taxonomy, the characterisation of L. acidophilus has struggled with misidentification and misrepresentation. In contrast, due to its global use as a probiotic supplement in functional foods, L. acidophilus sensu stricto is now one of the most well-characterised Lactobacillus species. Here, we establish the provenance of L. acidophilus strains, unpicking historical and current misidentifications of L. acidophilus, and reviewing the probiotic, genomic and physiological characteristics of this important Lactobacillus species.

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Bull MJ, Marchesi JR, Vandamme P, Plummer S, Mahenthiralingam E. Minimum taxonomic criteria for bacterial genome sequence depositions and announcements. Journal of Microbiological Methods 2012, 89: 18-21

Multiple bioinformatic methods are available to analyse the information encoded within the complete genome sequence of a bacterium and accurately assign its species status or nearest phylogenetic neighbour. However, it is clear that even now in what is the third decade of bacterial genomics, taxonomically incorrect genome sequence depositions are still being made. We outline a simple scheme of bioinformatic analysis and a set of minimum criteria that should be applied to all bacterial genomic data to ensure that they are accurately assigned to the species or genus level prior to database deposition. To illustrate the utility of the bioinformatic workflow, we analysed the recently deposited genome sequence of Lactobacillus acidophilus 30SC and demonstrated that this DNA was in fact derived from a strain of Lactobacillus amylovorus. Using these methods researchers can ensure that the taxonomic accuracy of genome sequence depositions is maintained within the ever increasing nucleic acid datasets.

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Garaiova I, Allen S. Probiotics – recent developments. Welsh Paediatric Journal 2008, 29: 18-21

In this article, the rationale behind the use of live microorganisms to improve health, recent developments in the classification and safety of the organisms and also the research studies undertaken are reviewed.

Garaiova I, Muchova J. Probiotics potential in diet. In Durackova Z (Ed): The role of natural components in the prevention and therapy of disease. Slovak Academic Press (SAP), Bratislava 2008, pg 219-233 (in Slovak)

Madden J, Hunter J O. A review of the role of the gut microflora in irritable bowel syndrome and the effects of probiotics. British Journal of Nutrition 2002, 88, Suppl: s67-s72. 

Irritable bowel syndrome (IBS) is a multi-factorial gastrointestinal condition affecting 8-22 % of the population with a higher prevalence in women and accounting for 20-50 % of referrals to gastroenterology clinics. It is characterised by abdominal pain, excessive flatus, variable bowel habit and abdominal bloating for which there is no evidence of detectable organic disease. Suggested aetiologies include gut motility and psychological disorders, psychophysiological phenomena and colonic malfermentation. The faecal microflora in IBS has been shown to be abnormal with higher numbers of facultative organisms and low numbers of lactobacilli and bifidobacteria. Although there is no evidence of food allergy in IBS, food intolerance has been identified and exclusion diets are beneficial to many IBS patients. Food intolerance may be due to abnormal fermentation of food residues in the colon, as a result of disruption of the normal flora. The role of probiotics in IBS has not been clearly defined. Some studies have shown improvements in pain and flatulence in response to probiotic administration, whilst others have shown no symptomatic improvement. It is possible that the future role of probiotics in IBS will lie in prevention, rather than cure.

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Minney S. Probiotics- the success story. Journal of Chemical Technology and Biotechnology 1991, 51 (4): 557-9

A role exists for the use of probiotic products as a prophylactic treatment for scouring in pigs.

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