Title Harnessing microbiome and probiotic research in sub-Saharan Africa: recommendations from an African workshop

To augment capacity-building for microbiome and probiotic research in Africa, a workshop was held in Nairobi, Kenya, at which researchers discussed human, animal, insect, and agricultural microbiome and probiotics/prebiotics topics. Five recommendations were made to promote future basic and translational research that benefits Africans. Introduction The rapid expansion of microbiome [1-5] and probiotic [6-9] research over the past 10 years and the many spinoffs providing novel insights into human and animal diseases, as well as products designed to alleviate them, have been primarily driven by sizeable funding from developed countries, especially Canada, USA and Europe. The first study conducted in Africa was based upon 16S rRNA gene sequencing, utilizing Illumina (San Diego, CA), and revealed a microbiome of relatively high diversity in the vagina of Tanzanian women infected with HIV [10]. This was followed by an intriguing study of children from a rural village in Burkina Faso, whose high-fiber diet is similar to that eaten in early human settlements at the time of the birth of agriculture [11]; compared to European children, the latter study found a significant enrichment in Bacteroidetes and depletion in Firmicutes (P < 0.001), with a unique abundance of bacteria from the genus Prevotella and Xylanibacter, enriched in bacterial genes for cellulose and xylan hydrolysis. Such continental-comparative studies can be revealing in terms of understanding how the environment and diet influence health, disease and weight gain, * Correspondence: [email protected] Lawson Health Research Institute and Departments of Microbiology & Immunology, and Surgery, University of Western Ontario, 268 Grosvenor Street, London, Ontario N6A 4V2, Canada Full list of author information is available at the end of the article © 2014 Reid et al.; licensee BioMed Central Lt Commons Attribution License (http://creativec reproduction in any medium, provided the or Dedication waiver (http://creativecommons.or unless otherwise stated. especially since it is known that modern diet and lifestyle can cause a dramatic change to the human gut microbiome [12]. Ironically, urban regions of Africa are transitioning towards a lifestyle and fast-food diet typical of ‘Westernized’ societies, potentially bringing with it an increased risk of metabolic diseases, such as diabetes. It will be interesting to see if the gut microbiome, shown to have a higher abundance of Bifidobacterium and a different BacteroidesPrevotella ratio at 6 months of age in resource disadvantaged Malawi compared to higher-income Finland, converts to one similar to Finland or the US [13]. Only minor differences were observed between the microbiota of subjects in Finland and Germany, emphasizing the African deviation [14]. This could have major implications as the microbiota affect energy extraction from food, possibly resulting in obesity. On the other hand, a particular nutritious diet might enhance beneficial microbiota to help lower the risk of diarrheal diseases and improve child health. This improved knowledge of the microbial composition provides a new focus to examine the consequences of intervention studies. The importance of this is illustrated by a Swiss-led study in Ivory Coast which showed that not only was iron fortification through biscuits ineffective for iron-deficiency anemia, but it worsened the unfavorable ratio of fecal Enterobacteriaceae to Bifidobacterium and Lactobacillus [15]. Other microbiome and comparative microbial genome studies have contributed to d. This is an Open Access article distributed under the terms of the Creative ommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and iginal work is properly credited. The Creative Commons Public Domain g/publicdomain/zero/1.0/) applies to the data made available in this article, Reid et al. Microbiome 2014, 2:12 Page 2 of 13 http://www.microbiomejournal.com/content/2/1/12 our understanding of adaptation mechanism of organisms in the environment [16] and how these might have been impacted by various niches [17,18]. Of particular interest is the gut microbiome of the malaria mosquito [19], perhaps as a first step in manipulating it to lower infectivity of the parasite. Fermented foods have a long history of use in Africa, and in recent years efforts have been made to identify the microbial strains and propagate them as probiotics to confer additional health benefits [20-23]. Some studies have shown the benefits of probiotics in the gut and vagina of HIV-infected patients in Africa [24,25], while in one report a combination of probiotic and prebiotic failed to resolve acute severe malnutrition in children from Malawi [26]. Knowledge gaps remain to be investigated with respect to African subjects. For example, studies which assess the male urinary tract microbiota have been conducted in Europe [27], but in Africa studies have examined the effect of circumcision on the corona sulcus microbiota. As the interchange of male and female microbiota may have important consequences for health, coordinating such studies amongst different populations would be worthwhile. In agreement with the sentiments brought forth by van Helden and colleagues [28] that humans, animals and the environment are inextricably linked and equal attention is needed to ensure optimal health for all, we convened a workshop in Nairobi, Kenya, at the International Livestock Research Institute (ILRA). The overall goal was to develop evidence-based concepts aimed at improving the health and wealth of people in African countries, with emphasis on mother and child, and local production and increased accessibility to nutritious and affordable products, integrated with effective education and training at community and academic levels. Three specific objectives of the workshop were: (1) discuss human, animal, insect, and agricultural microbiome as well as probiotics/prebiotics research in, or planned for, Africa; (2) engage African scientists and clinicians as well as help facilitate training focused on basic and translational research in the areas of microbiome investigations that promote sustainable, locally derived disease interventions; and (3) create new research initiatives and make recommendations to enhance African infrastructure, expertise and impact on these globally important areas. The outcomes and conclusions of the meeting are presented here. A cross section of researchers from across the world, with a track record in studying the microbiome and/or probiotics in Africa were invited. The meeting was limited to 40 participants for logistical reasons and to encourage discussion groups to form and come up with tangible concepts. With no funding to support travel of delegates, the reliance was upon goodwill and interest in the topic. Over 70 invitations were made to researchers based upon their publications in these areas, of which 40 accepted but eight cancelled too late for substitution, leaving a total of 32 participants from 10 countries. On day one, participants identified their interests and where they would like progress to be made. Topics for discussion were then agreed upon and day two was spent in groups to identify ways to move the topic forward. There was collective agreement that practical translational efforts should be prioritized that embrace local involvement and focus on sustainable outcomes. Cognizant of the realities of funding and the need to develop more African expertise and infrastructure, there was a commitment from all parties to collaborate and make the proposed projects actually happen. Figure 1 provides a summary of the essential components which the participants felt were needed for success, with education, training and research being absolutely essential. The following is a summary of the ideas, projects and recommendations from these discussions. We welcome interest and contributions by members of the larger scientific community who read this article. The extended microbiome of African indigenous cattle Cattle represent an integral part of society in many African countries as a source of meat and milk. Diseases of cattle have major implications for food security as well as community livelihoods and the economy. In addition, exposure of cattle to toxins, such as aflatoxins in maize or heavy metals in the soil, then become problematic for the consumer of their milk and meat, including offals. The cattle population is diversified with many breeds, but one important East African breed is the Boran which is both hardy and productive. Hypothesizing that the microbiome has an important role to play in productivity and health of cattle, five objectives were deemed important to better understand the microbiome composition. (i) Identify the normal microbiome (bacteria, archaea and fungi) of Boran cattle, their surface parasites as well as their feed and environment in three eco-climatic zones within Kenya. This would provide insight into seasonal effects, grazing conditions and help identify microbes associated with health. All sequencing will be performed at ILRI and added to the metadata of the Earth Microbiome Project (http://www.earthmicrobiome.org/). This will also build capacity by training graduate students at various East and Central African universities. (ii) Characterize the functional capabilities of microbial populations in the planktonic and mucosal surface of the rumen of Boran cattle. This will determine Handling toxins Fermented food, probiotics and health enhancement Human microbiome and prevention of diseases 5. DISTRIBUTION MARKETING COMMUNICATION 7. POLICIES, ETHICS AND GUIDELINES CHECK 1. RESEARCH 2. EVIDENCE BASED CONCEPTS