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Challenges and issues in analysing and interpreting microbiota sequencing data

Microorganisms in the intestine can have multifaceted effects on the health and productivity of animals and birds. The advancement in DNA sequencing technology has enabled scientists to study these microorganisms and their effects on unprecedented depth and scale. This resulted in thousands of studies about intestinal microbiota (term to describe all microorganisms in an environment) and their role.  This led to hundreds of commercial animal supplements with claims to positively modify intestinal microbiota to improve health and productivity. However, a depth of knowledge and skills is required to correctly analyse and interpret the sequencing data. There are several limitations and complexities in analysing such data and misrepresentation and misinterpretation of such data is common.

Scientists from the Institute for Future Farming System, Central Queensland University Australia have recently published a review entitled “the role of microbiota in animal health and productivity: misinterpretations and limitations” in the journal “Animal Production Science”. This review is focused on the issues and challenges regarding the analysis and interpretation of microbiota research. In addition, current trends in microbiota research in different livestock (specifically ruminants, pig and poultry) have also been discussed. 

The article has summarised the role of microbiota as “the most prominent and well-known roles include control of fat storage and weight gain, gut barrier defence, breaking down complex nutrients, development and training of the immune system, biosynthesis of vitamins and amino acids, communication with the nervous system, pathogen exclusion and control, mood, behaviour and food craving influence, short-chain fatty acid production and much more”.  Moreover, microbiota play specific roles during production stress such as heat stress, stress during transport, stress due to disease etc. 

The article emphasized that “the microbiota investigation is now a highly regarded methodology that solidified its role in livestock health and welfare research; however, the levels of complexity of each individual step, taken from animal trial to data analysis, need to be thoroughly understood and addressed.” The review has discussed how highly variable nature of microbiota population between animals and different gut sections, choice of marker genes and their specific regions and PCR primers affect the microbiota research. Similarly, the article has also highlighted the challenges in designing the microbiota research and selecting the right method and tools to analyse the data. The paper has affirmed that “regardless of the immense advancements in computational analysis tools, many factors in data analysis introduce biases and errors.”

The paper has concluded that “Despite some methodology shortfalls, microbiome research is far from slowing down, and a trend of shifting the focus towards animal and environmental welfare rather than productivity is emerging.”

The article can be accessed by clicking the article title below:

The role of microbiota in animal health and productivity: misinterpretations and limitations

Sustainability of Tourism in the Great Barrier Reef: Challenges and the Way Forward

Amrita Pudasaini Bajagai

The Great Barrier Reef  (GBR) is the iconic Australian reef in northern Queensland, which is world’s largest reef, and has been designated as a World Heritage Site in 1981 [1].  This area is called the financial lifeline of the coastal communities as millions of tourists visit this area every year for tourism and recreational activities [2]. A significant number of people in the GBR area are resource dependent to the reef, particularly served by the tourism industry [3]. Lately, there has been lots of attention about the degradation of the corals in the GBR region. Latest study reported the large scale bleaching of the reefs in the area particularly north of Cairns [4]. The reef region is in the verge of severe environmental, economic and social challenges like uncontrolled fishing, plastic waste, unplanned coastal development, overload of infrastructure etc., which need to be addressed by whole of users approach, education and proper resource planning for the sustainable tourism industry in the region. Sustainability of tourism in GBR region can be defined as operating of the tourism business in a way that the GBR maintains and improves its value now and for future generations with engagement of all stakeholders (Australian Government, 2015).
There are several environmental challenges to the GBR causing ecological degradation of the reef particularly multiple episodes of coral bleaching. Although the recurrent mass coral bleaching events have been believed to be associated with the global climate warming attributable to much more sophisticated and wider causes than tourism industry alone [4, 5, 6], some of the activities related to tourism industry directly or indirectly causes the degradation of the coral environment [7, 8]. Anthropogenic marine debris is another significant environmental problem influenced by the tourism in the GBR region [8, 9]. Recent study based on beach debris survey in the GBR region has found that there was widespread problem of marine debris throughout the region with up to 706 items recovered in one sample time on a beach [7]. This study has concluded that plastic fragments, cigarette butts, drinking straws, lollypop sticks, plastic bottles, wooden ice-cream sticks, chewing gum, balloon fragments and construction materials (bricks, tiles etc.) were the dominant debris type and the recreational boating and fishing were the most significant sources of such debris in inhabited and publically accessible islands. Such debris, particularly plastic waste, promote colonization of microbial pathogen in coral reef increasing the risk of coral reef diseases by up to 20 times [8]. Moreover, marine debris has been found detrimental to marine fauna like sea turtles [10] and seabirds [11]. Not only the debris but the tourist activities can also damage the corals on the reef [12]. Intensive recreational diving and snorkeling on coral reefs increases coral diseases by up to 3-fold as compared to lower recreational activities in reefs [12]. The effects on corals and sea fauna consequently could affect the inflow of visitors causing negative effect to the tourism industry. Other environmental challenges in the reef region are deterioration of water quality from land-based runoff, unplanned coastal development and over-fishing [4, 13]. These environmental challenges should be addressed on priority basis to maintain the aesthetic, ecological and economic value of the GBR for sustainable tourism industry in the region.
In addition, tourism industry in GBR has some economic challenges to impede the sustainability of this industry in this region. Marshall and colleagues [3] has recently reported that tourism business operators in the GBR region were overly resource dependent. Resource dependency is an economic concept that describes the relationship between particular groups of people with natural resources. A community is resource dependent when that community is economically, socially and culturally dependent on the resource they have been exploiting and they do not have easy alternatives if that natural resource were changed or could not provide the initial function [14]. Tourism operators are economically dependent on the GBR and they are not flexible to secure other forms of employment due to their age; lack of education; number of dependents; duration in the industry and region [3]. This lack of flexibility influences their resilience and make them more vulnerable during unexpected conditions [15] forcing them to exploit the resources or depend on welfare. This form of resource dependency should be considered while thinking about the sustainability of the whole system. To achieve the sustainability of tourism industry in the GBR, the real cost of the industry should be explored in broader sense analyzing the cost of the tourism industry in the environment, local community and the indigenous people because economic benefit from a booming industry sometime may have unintended negative consequences to the people and community outside of the industry as evidenced by the impacts of mining industry in Western Australia [16]. Therefore, there should be an in-depth study about the economic impact of tourism on the community outside the tourism business.
Moreover, tourism industry in GBR also has some social challenges to consider for the sustainability of the industry. One of the major social challenges is the conflicting values about the GBR among the local community and tourism business operators [17]. Community defined benefits of reefs could be different from generally perceived economic and ecological benefits. Local community members value undeveloped and rubbish-free beaches, clean ocean water, reef fish, mangroves and coral reefs more than the reef tourism [17]. Clean and clear ocean with healthy reef is the most important for the local community than being able to exploit the reef for economic benefit [17]. Also, people or community independent of the reef (neither the local communities nor the business operators) may have different perception about the value of the GBR as they could see the reefs as protector of storms and large scale nutrient recycler [18, 19].  This contrasting understanding of values could create conflict between communities outside the tourism industry and tourism business operators. Although no study was found about the effect of tourism on local infrastructures, increasing number of inbound visitors may increase the pressure on road, emergency services, local parks etc. Furthermore, local communities in the GBR region are equally sensitive to preserve the indigenous cultural values [17]. Increased overseas and interstate tourists movement could have negative impacts on traditional culture and values of the indigenous people.
The environmental, economic and social challenges as discussed above should be addressed for the sustainability of the tourism industry in the GBR region.  Eenvironmental challenges should be dealt with urgently as protection of health and integrity of this iconic world heritage site very crucial for its value beyond the tourism. Engagement of all stakeholders in the planning, implementing, monitoring and evaluation phase is important for any plan to be success therefore whole of users approach should be applied to plan and implement any sustainability interventions [2]. Adequate resource allocation and targeted strategic communication to the concerned stakeholders is also paramount [6, 20]. Government should focus on policy and collective actions for environmental protection such as use of renewable energy, efficient land management, and proper waste disposal [6]. In addition, creating the awareness about the sustainable tourism among all stakeholders including visitors and local community is also important. Therefore, it is important to include such information in the curriculum of the students in the GBR region to create awareness among future generation about sustainable reef environment. A triad demonstrating the relationship among economic, environmental and social dimensions of sustainability as proposed by Herremans an Reid [21] could be helpful to analyze the issue and to be used as a tool to teach students the concept of sustainable reef ecosystem. Such tool could be helpful to analyse the perception value of the GBR by different stakeholders and possible conflicts between perception of one stakeholder’s to that of another [21]. For example, as presented above the value of coral reef to the local community is different from the value to tourism business operators and could be conflicting to each other [17]. An education material can be designed to deliver to the students of the GBR region, which discusses all of these issues in the context of their own values, which help them to understand the issue in broader sense. Australian Government has prepared a long-term sustainability plan for the GBR called ‘Reef 2050 Long-Term Sustainability Plan’ based on research, lesson learned from past programs and the recommendations from the World Heritage Committee [2]. Effective implementation of this plan could help the sustainability of all uses of the GBR including tourism industry in the region.
In conclusion, Great Barrier Reef is the iconic world heritage natural resource in northern Queensland, which support the livelihood of millions of people through tourism industry. There are several environmental, economic and social challenges for the sustainability of tourism industry in the GBR region. Degradation of coral ecosystem including recurrent mass coral bleaching is the most prominent environmental issue, which is mainly caused by global climate warming and supported by several other tourism related activities. Anthropogenic marine debris, intensive diving and snorkelling, water quality deterioration by surface water runoff, unplanned coastal development and uncontrolled fishing are some environmental issues associated to tourism industry.  Similarly, resource dependence of tourism operators is the major economic issue to be considered followed by other possible economic issues like negative impact of tourism to the community outside the tourism industry. Moreover, there is conflict about the perceived value of the reef between tourism operators and community members as one of the social challenges. These issues should be addressed based on the consultation with all concerned stakeholders using whole of system approach. There should be adequate investment, targeted communication and effective education for the sustainability of tourism industry. Awareness created through effective education, adequate resource allocation and engagement of all stakeholders help to maintain and improve the value of the Great Barrier Reef now and for future generations.